Entering edit mode
Alex Sanchez
▴
20
@alex-sanchez-2852
Last seen 10.2 years ago
Hello
I have a doubt about how to use frma.
I have 30 hgu133plus2 arrays where I would like to find the
"unexpressed" genes. If I have understood it well the "barcode"
function in the frma package can be used to find such genes, or, say
provide a proposal.
The arrays have been obtained in two different batches so frma seems
even more approprite because ir claims to have the ability to process
data from different batches.
My question is then how should I proceed.
My idea is
- Process every batch (two in this case) separately
- Combine the data inti a single object
- Use barcode on this object to call the unexpressed genes.
Can someone confurm me If this is the right approach?
thanks for the help
Alex Sanchez
Statistics Department. Universitar de Barcelona &
Statistics and Bioinformatics Unit. Vall d'Hebron Research Institute
Enviado desde mi iPhone
El 03/03/2012, a las 12:00, <bioconductor-request at="" r-project.org="">
escribi?:
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>
> Today's Topics:
>
> 1. Provide an Example for AnnotatedDataFrame (Deepak Datta)
> 2. Re: Difficulty in AnnotatedDataFrame (James F. Reid)
> 3. Re: easyRNASeq error (Nicolas Delhomme)
> 4. Biobase typo in example of AnnotatedDataFrame man page
> (James F. Reid)
> 5. Re: Biobase typo in example of AnnotatedDataFrame man page
> (Martin Morgan)
> 6. Re: easyRNASeq error (Nicolas Delhomme)
> 7. Re: A problem about trimLRPatterns (wang peter)
> 8. Summarizing Single-channel Agilent data (David Westergaard)
> 9. Gene-Metabolite correlation network (pankaj borah)
> 10. Re: problem creating own org.Ss.eg.db (Hooiveld, Guido)
> 11. Re: Summarizing Single-channel Agilent data
> (axel.klenk at actelion.com)
> 12. Re: Gene-Metabolite correlation network (Sean Davis)
> 13. Re: Gene-Metabolite correlation network (pankaj borah)
> 14. Re: A problem about trimLRPatterns (Harris A. Jaffee)
> 15. KEGGSOAP (Ricardo Silva)
> 16. GAGE heatmap pdf question... (Alan Derr)
> 17. Re: Finding coding SNPs with predictCoding (Valerie Obenchain)
> 18. Re: Finding coding SNPs with predictCoding (Thomas Girke)
> 19. Re: KEGGSOAP (Martin Morgan)
> 20. unable to readImage using EBImage package (diyanah [guest])
> 21. Re: unable to readImage using EBImage package (Dan Tenenbaum)
> 22. beadarray vignette has broken code in R2.14.1? (Henriquez,
Nick)
> 23. Re: Gene-Metabolite correlation network (B Usadel)
> 24. Re: Gene-Metabolite correlation network (B Usadel)
> 25. Warning of function "ncbiTaxonomy" (???)
> 26. Re: how edgeR control outliers? (Yuan Tian)
> 27. Re: beadarray vignette has broken code in R2.14.1? (Dan
Tenenbaum)
>
>
>
----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 2 Mar 2012 16:29:54 +0530
> From: Deepak Datta <deepaktheinvincible at="" gmail.com="">
> To: bioconductor at r-project.org
> Subject: [BioC] Provide an Example for AnnotatedDataFrame
> Message-ID:
> <cahzx1smq_wujujhithkt8fhn9cq1wvfdjcuyfy9h9uyy4=shra at="" mail.gmail.com="">
> Content-Type: text/plain
>
> hii... this is Deepak....
>
> i am working on analysis of microarray data using bioconductor and i
am
> rank amateur in R
>
> I tried using this code snippet
> phenoData(spikein95) <- new("phenoData", pData = pd, varLabels = vl)
>
> but it said that phenoData is now defunct and we need to use
> AnnotatedDataFrame. And i am not able to proceed because of the
following
> error
>
> AnnotatedDataFrame(x1)<-new("AnnotatedDataFrame",pData=pd,
varLabels=v1)
> Error in .nextMethod(.Object, ...) :
> invalid names for slots of class ?AnnotatedDataFrame?: pData,
varLabels
>
>
> i am basically trying to segregate the samples into 3 parts
containing
> normal, HSIL and SCC data and this is the code that i have used till
now...
>
> setwd("E:\\Project\\CEL files\\Old\\GSE7803-3")
>> f1=list.celfiles(path="E:\\Project\\CEL files\\Old\\GSE7803-3")
>> x1<-ReadAffy(filenames=f1)
>> pd <- data.frame(population = c(1,1,1,1,1,1,1,1,1,1,2, 2,
> + 2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3),
> + replicate= c(1,2,3,4,5,6,7,8,9,10,1,2,3,4,5,6,7,
> + 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21))
>> rownames(pd) <- sampleNames(x1)
>> v1 <- list(population = "1 is normal, 2 is HSIL, 3 is SCC",
> replicate="arbitary numbering")
>
>
> i further wish to perform rma and then generate a MA plot.
>
> kindly help me rectify this error and please explain with an
*example* so
> that i could proceed further.
>
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 02 Mar 2012 11:03:37 +0000
> From: "James F. Reid" <james.reid at="" ifom-ieo-campus.it="">
> To: Deepak Datta <deepaktheinvincible at="" gmail.com="">
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] Difficulty in AnnotatedDataFrame
> Message-ID: <4F50A909.1020602 at ifom-ieo-campus.it>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hi Deepak,
>
> please keep the thread on the list for other users.
>
> On 02/03/12 10:28, Deepak Datta wrote:
>> hey James, i have read the help page and i did not find it helpful.
i
>> would really appreciate if you could please explain me with an
example
>> giving details on creating a metaData
>
>
> something like this should work:
>
> new("AnnotatedDataFrame",
> data=pd,
> varMetadata=data.frame(labelDescription=unlist(v1)))
>
> since your v1 is a list (it needen't be).
>
> Best.
> J.
>
>>
>>
>> On Fri, Mar 2, 2012 at 3:49 PM, James F. Reid
>> <james.reid at="" ifom-ieo-campus.it="" <mailto:james.reid="" at="" ifom-ieo-="" campus.it="">>
>> wrote:
>>
>> Hi Deepak,
>>
>> you need to construct an AnnotatedDataFrame in the following
way:
>> AnnotatedDataFrame(data=df, varMetaData=metaData)
>> Look-up the help page which is well documented:
>> help("AnnotatedDataFrame")
>>
>> HTH.
>> J.
>>
>>
>> On 02/03/12 10:11, Deepak Datta wrote:
>>
>> hii... this is Deepak....
>>
>> i am working on analysis of microarray data.
>>
>> We tried using this code snippet
>> phenoData(spikein95)<- new("phenoData", pData = pd,
varLabels = vl)
>>
>> but it said that phenoData is now defunct and we need to use
>> AnnotatedDataFrame. And i am not able to proceed because of
the
>> following
>> error
>>
>> AnnotatedDataFrame(x1)<-new("__AnnotatedDataFrame",pData=pd,
>> varLabels=v1)
>> Error in .nextMethod(.Object, ...) :
>> invalid names for slots of class ?AnnotatedDataFrame?:
pData,
>> varLabels
>>
>>
>> i am basically trying to segregate the samples into 3 parts
>> containing
>> normal, HSIL and SCC data and this is the code that i have
used
>> till now...
>>
>> setwd("E:\\Project\\CEL files\\Old\\GSE7803-3")
>>
>> f1=list.celfiles(path="E:\\__Project\\CEL
>> files\\Old\\GSE7803-3")
>> x1<-ReadAffy(filenames=f1)
>> pd<- data.frame(population = c(1,1,1,1,1,1,1,1,1,1,2,
2,
>>
>> + 2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,__3,3,3,3,3,3,3,3,3,3,3),
>> + replicate= c(1,2,3,4,5,6,7,8,9,10,1,2,3,__4,5,6,7,
>> + 1,2,3,4,5,6,7,8,9,10,11,12,13,__14,15,16,17,18,19,20,21))
>>
>> rownames(pd)<- sampleNames(x1)
>> v1<- list(population = "1 is normal, 2 is HSIL, 3 is
SCC",
>>
>> replicate="arbitary numbering")
>>
>>
>> i further wish to perform rma and then generate a MA plot.
>>
>> kindly help me rectify this error and if possible explain
with
>> an example
>> so that i could proceed further.
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>>
>> _________________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org="">
>> https://stat.ethz.ch/mailman/__listinfo/bioconductor
>> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">
>> Search the archives:
>>
http://news.gmane.org/gmane.__science.biology.informatics.__conductor
>>
<http: news.gmane.org="" gmane.science.biology.informatics.conductor="">
>>
>>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 2 Mar 2012 12:20:36 +0100
> From: Nicolas Delhomme <delhomme at="" embl.de="">
> To: "Davis, Wade" <davisjwa at="" health.missouri.edu="">
> Cc: Bioconductor mailing list <bioconductor at="" r-project.org="">
> Subject: Re: [BioC] easyRNASeq error
> Message-ID: <8395D3FF-9D14-49E1-855F-E578A39E3089 at embl.de>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Wade,
>
> I'll send you the package off-list. And discuss how we can do for
the data as it's still interesting for me to enhance my chromosome
name validity checks.
>
> Cheers,
>
> Nico
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> Genome Biology Computational Support
>
> European Molecular Biology Laboratory
>
> Tel: +49 6221 387 8310
> Email: nicolas.delhomme at embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
> ---------------------------------------------------------------
>
>
>
> On 1 Mar 2012, at 23:14, Davis, Wade wrote:
>
>> Hi Nico,
>> If you could send me a windows zip that I could try out the changes
now instead of waiting for them to get pushed through in a few days.
But I don't mind waiting, whatever is easiest for you.
>>
>> I've been in a workshop all days, so I haven't gotten a chance to
try out the suggestions for the second problem, but I will do so and
get back to do.
>>
>> Also, you asked for a sample file to help with the second problem.
I'm not sure if you still want or need that, but below is the first 60
lines or so. I can send you an entire file (compressed which is about
455MB) if you think that would be helpful.
>>
>> Thanks!
>>
>> Wade
>>
>> HWI-ST538 160 7 1101 1635 1954 ACAGTG 1 GAT
ATCTNNNNNNGAAGAAAACGAGGGAGATTCCAAGGCCGAGCAGCTACACCNGGTACAGAAGCAGTCTGCC
ACTTTGCCCTCGCCCATCACCCACTCC
>> BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC
N
>> HWI-ST538 160 7 1101 1661 1972 ACAGTG 1 GGA
TAGCATNNNAAATGTAAATGAGGAAAATACCTAATAAAAAATATTAAAAAAAAAAAAGACACCGCCAGGA
ACTTGTGAGAAATCCAAATTCTACATT
>> [[[______BBBQQX_^^^^_^___^]^_^^^^[^^^^^^]^^^^^^^^^^^^^^^^BBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC
N
>> HWI-ST538 160 7 1101 1949 1944 ACAGTG 1 AGG
GGTTNNNNNNTTCAAGACCTCTCCCCTGNNGAGAAAGAAACCCAAGCAGNNGCCTGTGGGAGGGAACACG
GACCTGACACCTCTGCCTCAGACTCCT
>> [[XZY_^BBBBBBQQ[\Z\]_[[Z^^]^^[^BBOL[\X^^PY]ZX\^BBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC
N
>> HWI-ST538 160 7 1101 1820 1948 ACAGTG 1 GTC
AGCTNNNNNNAGGGTCCGATCGTATTGGANGAGGATATCTTTGATCTCCNNCTTGGAGGCTTCATCCACA
TATTTTTGGTAATAAGCTACCAGGGCC
>> [[[^___BBBBBBRS]_]^__^__^^^^^^^^BO[\^^^^^^^^^\^^^^^]BBLW\\^]_^X^^]\
]]]]^^]]]]]^\[VZZ\\\\Y[\\\[\[[Y[[ QC
N
>> HWI-ST538 160 7 1101 1773 1957 ACAGTG 1 CTT
TGGTTNNNNNGACCTCGCTTGTAGCCAGCAAAAATGGCCTTGCACCACAGCCTTCCAGACATACTTGCTG
TTAGAAGTCCTGAGATCGGAAGAGCAC
>> WZZ_[\]_BBBBBRQY_^^\Z^__^^^^^^]^]^]^^^^^^]^^^]]X]]]^^^^^^^___[^^]]^
^^]^^W\\]]]\]V\\\][[[\\[[Z[Y[[WZW QC
N
>> HWI-ST538 160 7 1101 1971 1962 ACAGTG 1 CTT
TGTTTNNNNTCTGGTCACAATAGTTGGGGGCAGAAAAGACAGTGACACAGCGGCCACCATGGGCCACCTC
GTAGCCCTCGGCTTTGACTTCATGGCT
>> [[[_____BBBBRR_____^__^________^^^^^^^^^^^^^^^^^^^^^^[^^\\[[^[[[\[[
[[[[[[[W[[[\\[[WY[[U[YT[[\[YZSYW[ QC
N
>> HWI-ST538 160 7 1101 1878 1976 ACAGTG 1 CCG
CTGTCTTNCTCAGGAAGCACGCATTTCCACAGGCCATAGGGCTTTCCTACCACAGTTTGCCACAATCTCA
ATGTCCCATCTTCAGAACCGCTGGCAT
>> ^W^\cc\`^`BQQ``JY[YRb`^_dUccaSccaIYHOWOXRacQaaQabd\bbcbbcc\^bccc]Z^
c_]R_````UZZ]`Y\ZT]]`BBBBBBBBBBBB RM
N
>> HWI-ST538 160 7 1101 1934 1999 ACAGTG 1 CTC
CACTGAAGTACTTCAGGTAGTAGTCCATGACGCCCTTGTCGTCGGTTCGCGACTCCTCATCACTGTCCCC
GGCCCGGCCCACCGATGACATCATCTG
>> bbbeeeeegggeghiiiiiigghgfiiiiihihiihiihiihhfghdgZeefhadeecdbdb`bccb
b`bb`aQX[acX[[acO[aOEHOGYRY`]Y`R] chr10.fa 80607676 R
100 500 Y
>> HWI-ST538 160 7 1101 2013 1948 ACAGTG 1 CAC
ATCTNNNNNNCCATGGAGCAGATTGAAGANGAAATCAAAGGTTGTTTGGNNTTTCTTCGCACAGTATATA
GTGTCTTTGGATTTTCATTTAAATTGA
>> [[[___^BBBBBBRSX_____^_^_^_^__^^BP[^^^^^^^^^\^^^^^^[BBLW\^^__]^^^^^
Z\]]]]^\Z\]]^^][[\\\\\\\\\\\\[\Y[ QC
N
>> HWI-ST538 160 7 1101 2064 1957 ACAGTG 1 AGA
AAGTTNNNNNATAGAAGATGTATAAGTTGATCGTAACGGAAGCGTGGATAAGATGCTCGGATCCATAGGA
ATGTTGATGATAGTAGTAGAGCTTCTA
>> [[[[^[\_BBBBBQQ\[\^]__^[_]_^^^_^^__^[^^[[W^^[^^\^^\^^^]^^^___[^[XW]
Z]^^BBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC
N
>> HWI-ST538 160 7 1101 2129 1991 ACAGTG 1 GTA
ATATTCATTTAGCCTTCTGAGCTTTCTGGGCAGACTTGGTGACTTTGCCAGCTCCAGCAGCCTTCTTGTC
CACAGCTTTGATGACACCCACAGCAAC
>> ___ce`cce`ggfdhfhfgbfbefdghggfd`ff]eZegg]eIYYYceg^cedfce^ebgfce_ccf
hdfdZbdbV`db]Za^ZaZ]__bbaa_PTGT^` RM
Y
>> HWI-ST538 160 7 1101 2267 1959 ACAGTG 1 CAG
CACAGNNNNGATGGCTACGTACATGGCTGGGGTGTTGAAGGTCTCAAACATGATCTGGGTCATCTTTTCA
CGGTTGGCCTTAGGGTTCAGGGGGGCC
>> [[[__^^^BBBBQQ_\^[^]^^^^^[^_^[^^^^^\Z\^RU\]]UY]WXZ^]Z^]Z]^_^^]ZZV^B
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC
N
>> HWI-ST538 160 7 1101 2466 1999 ACAGTG 1 CGT
ACTTCTCCCACTCGCTTGTGCTCTGTCACTAGAAGGTTATTCTTGAAAGGTTCTGTGCCTTTTTCTTCAG
GCTTCATCTGTCATACCTCTACTTGAT
>> bbaeeeeegggggiiifiiiihiiiiihhhiiihighiiafgfhiiifaehghXcghhhhbghiiii
fhhfdghhgfedgeddcbeeccbddd`c_b`cc chr7.fa 54159980 R
100 504 Y
>> HWI-ST538 160 7 1101 2566 1981 ACAGTG 1 ATT
GAACTCANCTCCTTTTAGGTTGCCCTACTAACTGGACATTGTGGACACTAAATCATATTGGGGTGATGAA
TAATCAAATTTTCAATATCAAACAATG
>> abaceeeeggBQ`eghhiifhhiiigihifhihfhhihhiifhffdgffhifhihfhhhiihdgfgZ
d^bd^ade^abddc]`bc__bcdc_c_bb`abb chr10.fa 66474748 R
10G89 497 Y
>> HWI-ST538 160 7 1101 2943 1957 ACAGTG 1 TCC
GAATANNNNNCGGTCAAAATAAAAGCTCAAGATGACATCAGTCCCATTTGTCCTAAGTCCTGGTGTTGTA
TGGATGGTAAGCAGCAGCCAATTATGG
>> [[[^^^^_BBBBBQQ_\_^___^_^_^^^^^^^^^^^^^^^^^^\^^^^^^^^^^^^^__\]^]^_]
^^^^^_^_^^^^^W\]Z]]][[^[[[[W[\\\[ QC
N
>> HWI-ST538 160 7 1101 2883 1967 ACAGTG 1 ATC
AGACTCNNNCTGCACGTTCACACCATAAGTCTCATCAATGTTGTCATCCATATTCTGTATCTCCTTGTCG
CCACCGTAGTCTGTGATCTTCTTGCCC
>> [[[__^^^^BBBR[T]]^^][]]^^[X][]]W^]^^^^X[Y\[YRY^[^^^^[]^^^^]^\Y]\Z^^
[[ZU\\^BBBBBBBBBBBBBBBBBBBBBBBBBB QC
N
>> HWI-ST538 160 7 1101 3133 1960 ACAGTG 1 CTC
TCAAANNNNCTACAGAGCCCAGGAAGATTTCAGGATGAAGAGCTTCCTCCTCTTCCTCACTATCATTCTT
CTGGTTGTGATTCAGATACAAACAGGA
>> [[[^Z]_]BBBBSQ\_Z^_^_^^_^^^]_^^^^\^^^[Z]^^^^^^]^^^^^^]^]^^_]^ZZY^^_
\]^\]^[]Z\^^Z\\]\\\\\\\]]]]\[[VQV QC
N
>> HWI-ST538 160 7 1101 3023 1964 ACAGTG 1 GGC
CACTCTNNNTTGTGCCTTCCACACCTTTTGGTGCAGATTGTTCAGTGGGGAGCTGCCTCATATTCTCTGA
CTGGCCAGAAAGGCTCTCGCTGGGGTT
>> [[[__^^^^BBBRQ_\_^^___^^^^_^^__^]^^^^^^^^^^^]\^^]^^^^^^^^^T]^^ZZ^\^
]^^^]\\]]^BBBBBBBBBBBBBBBBBBBBBBB QC
N
>> HWI-ST538 160 7 1101 3219 1966 ACAGTG 1 CAG
ATGTGTNNNAATGCTAGGTGTGGTTGGTTTATTCCTAGCGTCACTATTATCAGGCCTAGTTGGCTTGATG
TAGAGAAGGCAATGATTTTTTTGATGT
>> [[[^_____BBBS[]___^__[_]_^\__^Z]^^^^^^^^^^^^^^^^^^^^^^]^^^^_[^^^^__
_^[^^]]]\\]\]]^^[[\\\\\\\\YXTW[\\ QC
N
>> HWI-ST538 160 7 1101 3047 1993 ACAGTG 1 CTC
TTGTGTCCGTTTTCTTGCTGTAGCGTTTTCTCCGTACCACTCACTGATACCTGTCTATCGACTACGTGGG
ATGGCAGAGGCACTGCCAGGCTCCACA
>> bbbeeedegggfghiiiihhiihifhiieggihffh[affgcgfebb]eefdfh[bgbcdfe_fW^\
]aaZa`abZ^``a_GWWW^```^bS^`W^^BBB chr1.fa 154218045 F
100 36 Y
>> HWI-ST538 160 7 1101 3462 1958 ACAGTG 1 CCA
CTCGTNNNNCTTGCGATCATTGTGCTTAGGGTCTTCTGATACATCTGGGGGAACATCTGTTTTATCTGAA
CAAGGTCAATCTCACTTCGAGTGACCA
>> [[[^^^_\BBBBQQ[ZZ^_[Y_[_]_\W^^^^[^M[]]]]\]]^^^^]\^^^FZF\\]Z^^^X\^^^
]]^]\Z\]ZOZXZZ[\\\\TZU\[ZTTW[\[\\ QC
N
>> HWI-ST538 160 7 1101 3261 1972 ACAGTG 1 CCT
GGATGTNNNCGTGGATCGGGTCTTGAACGTGGACTTGCCGCACCTTGTATCTCAAGCCCAGCGCCACACC
CTTGCTGACTTTCTGAACACTACTGTC
>> BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC
N
>> HWI-ST538 160 7 1101 3390 1979 ACAGTG 1 TGC
AGTTCTTNCCCGTGGCTCCTGAGCCAGCAATGTCGTCTGGGAAGCCATCATCAGCTCATTCAGCTGAGAC
GTGCTAGAGGTCTCCTCAGCTTGGAGC
>> bbbeeeeeggBRbfgfhihiiihhhhiiiiiehhichhgggfghbgedgdffhffdefff`bd]bdf
edceecdZZ`_`bb_aL[bcc`b]`b]`b_`[` chr1.fa 187111962 F
10T89 497 Y
>> HWI-ST538 160 7 1101 3666 1959 ACAGTG 1 CCG
AACACNNNNCCCGGATCTCATCTCACAGAATCGTGGGTACGTCTGAACCAGCTGGTTGCCCCCAAAAATT
ACCTGTTTCACGCCCCTGGTGCAGCCC
>> BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC
N
>> HWI-ST538 160 7 1101 3667 1975 ACAGTG 1 AGA
ACACCGANGTCCACCTTCAAGTTAGGGGAAATGGCATATTCTTCGATCGGCTTGCTGATTTGGGAAATTT
TATCCTTGACTGCTTCTGGAGCAGGAC
>> PZZTTP_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB chr4.fa 99634649 R
10G3T10C4C19T1T13A10AG3T17 77 N
>> HWI-ST538 160 7 1101 3986 1969 ACAGTG 1 ATT
AAATCTNNNCATGCTCTGAAAAAGGCTTTAGGTCACTCCAAGCTTGGCAGTTAACATTTGGCATGGACAC
TGGTAAAACCACAATAGAGAAAGAAGT
>> [[[^_____BBBRY__^^^__^^^^^_^^__^^^^^^^^^]^^^^^^^]^^^^\^^^^____]^___
_[^^[^^^^Z^Z\\\\^[^^^]]\[\\\\[[[R QC
N
>> HWI-ST538 160 7 1101 4230 1977 ACAGTG 1
CGCCTCCGGGNCGTGGCACTCTGGGGCTCTGCCGTCGACATGGGCGCCGCC
