QuasR question
0
Entering edit mode
@michael-stadler-5887
Last seen 7 days ago
Switzerland
Dear Dani, I hope you don't mind me cc'ing the bioconductor list. The question may be of interest to others. The answer to your questions is described in the vignette (section 5.1 "Create a sample file"). Essentially, you just list the pre-existing bam files instead of the sequence files. QuasR will then use these instead of creating new bam files. Let me know if that is not clear. Best, Michael On 01.09.2014 09:49, Daniel Soronellas wrote: > Dear Dr. Stadler, > > I contact you because I recently found the QuasR R package, which I found to be very interesting and I would like to apply in my downstream analysis for different experiments (mainly ChIP-seq). > I have BAM files which are already mapped by a custom pipeline, and I wanted to use QuasR from this starting point. I searched on the documentation how I can load already mapped files but didn't find the answer, is it possible for you to write a few lines of code as an example of BAM file loading to the QuasR package? > > Thank you very much for your time and attention, > I would really appreciate any help you can give > > Sincerelly, > Dani Soronellas > Chromatin & Gene Expression Lab > Ph: 933160115 / Ext: 1115 > @: daniel.soronellas at crg.eu > Center for Genomic Regulation, PRBB > Av. Doctor Aiguader, 88 > 08003, Barcelona (Spain) >
QuasR • 953 views
ADD COMMENTlink
0
Entering edit mode
@daniel-soronellas-6720
Last seen 6.5 years ago
Dear Dr. Stadler, Thank you for your quick answer. I was reviewing section 5.1 from the tutorial, specifically the sub- section: [ Working only with BAM files after performing alignments ] where it shows that sampleFile2 is a bam file. Then I tried my own BAM file: genomeFile <- "genome.fa" sampleFile2 <- "chr22.bam" proj2 <- qAlign(sampleFile2, genomeFile) and got the following error: Error in read.table(file = file, header = header, sep = sep, quote = quote, : more columns than column names In addition: Warning message: In read.table(file = file, header = header, sep = sep, quote = quote, : line 1 appears to contain embedded nulls Do you know how I can solve it? Thank you very much for your time and support, Sincerelly, Dani Soronellas Chromatin & Gene Expression Lab Ph: 933160115 / Ext: 1115 @: daniel.soronellas at crg.eu Center for Genomic Regulation, PRBB Av. Doctor Aiguader, 88 08003, Barcelona (Spain) ________________________________________ De: Michael Stadler [michael.stadler at fmi.ch] Enviat el: dilluns, 1 / setembre / 2014 10:03 Per a: Daniel Soronellas A/c: bioconductor at r-project.org Tema: Re: QuasR question Dear Dani, I hope you don't mind me cc'ing the bioconductor list. The question may be of interest to others. The answer to your questions is described in the vignette (section 5.1 "Create a sample file"). Essentially, you just list the pre-existing bam files instead of the sequence files. QuasR will then use these instead of creating new bam files. Let me know if that is not clear. Best, Michael On 01.09.2014 09:49, Daniel Soronellas wrote: > Dear Dr. Stadler, > > I contact you because I recently found the QuasR R package, which I found to be very interesting and I would like to apply in my downstream analysis for different experiments (mainly ChIP-seq). > I have BAM files which are already mapped by a custom pipeline, and I wanted to use QuasR from this starting point. I searched on the documentation how I can load already mapped files but didn't find the answer, is it possible for you to write a few lines of code as an example of BAM file loading to the QuasR package? > > Thank you very much for your time and attention, > I would really appreciate any help you can give > > Sincerelly, > Dani Soronellas > Chromatin & Gene Expression Lab > Ph: 933160115 / Ext: 1115 > @: daniel.soronellas at crg.eu > Center for Genomic Regulation, PRBB > Av. Doctor Aiguader, 88 > 08003, Barcelona (Spain) >
ADD COMMENTlink
0
Entering edit mode
@michael-stadler-5887
Last seen 7 days ago
Switzerland
Dear Dani, Please have a look at the documentation of qAlign. The sampleFile argument takes the path and filename of a text file, which in turn contains the paths and file names of the sequence or bam files. What you do is to directly pass the bam file name, which is not the same. QuasR comes with a few example sample files. I suggest that you copy one of those and edit it to contain your bam files. You can get the path to such a sample file on your system by: system.file("extdata/samples_chip_single.txt", package="QuasR") Best, Michael On 01.09.2014 10:25, Daniel Soronellas wrote: > Dear Dr. Stadler, > > Thank you for your quick answer. > I was reviewing section 5.1 from the tutorial, specifically the sub- section: > > [ Working only with BAM files after performing alignments ] > > where it shows that sampleFile2 is a bam file. Then I tried my own BAM file: > > genomeFile <- "genome.fa" > sampleFile2 <- "chr22.bam" > proj2 <- qAlign(sampleFile2, genomeFile) > > and got the following error: > > Error in read.table(file = file, header = header, sep = sep, quote = quote, : > more columns than column names > In addition: Warning message: > In read.table(file = file, header = header, sep = sep, quote = quote, : > line 1 appears to contain embedded nulls > > Do you know how I can solve it? > > Thank you very much for your time and support, > Sincerelly, > Dani Soronellas > Chromatin & Gene Expression Lab > Ph: 933160115 / Ext: 1115 > @: daniel.soronellas at crg.eu > Center for Genomic Regulation, PRBB > Av. Doctor Aiguader, 88 > 08003, Barcelona (Spain) > ________________________________________ > De: Michael Stadler [michael.stadler at fmi.ch] > Enviat el: dilluns, 1 / setembre / 2014 10:03 > Per a: Daniel Soronellas > A/c: bioconductor at r-project.org > Tema: Re: QuasR question > > Dear Dani, > > I hope you don't mind me cc'ing the bioconductor list. The question may > be of interest to others. > > The answer to your questions is described in the vignette (section 5.1 > "Create a sample file"). Essentially, you just list the pre-existing bam > files instead of the sequence files. QuasR will then use these instead > of creating new bam files. > > Let me know if that is not clear. > > Best, > Michael > > On 01.09.2014 09:49, Daniel Soronellas wrote: >> Dear Dr. Stadler, >> >> I contact you because I recently found the QuasR R package, which I found to be very interesting and I would like to apply in my downstream analysis for different experiments (mainly ChIP-seq). >> I have BAM files which are already mapped by a custom pipeline, and I wanted to use QuasR from this starting point. I searched on the documentation how I can load already mapped files but didn't find the answer, is it possible for you to write a few lines of code as an example of BAM file loading to the QuasR package? >> >> Thank you very much for your time and attention, >> I would really appreciate any help you can give >> >> Sincerelly, >> Dani Soronellas >> Chromatin & Gene Expression Lab >> Ph: 933160115 / Ext: 1115 >> @: daniel.soronellas at crg.eu >> Center for Genomic Regulation, PRBB >> Av. Doctor Aiguader, 88 >> 08003, Barcelona (Spain) >>
ADD COMMENTlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 141 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.4