User: Hadi Gharibi

gravatar for Hadi Gharibi
Reputation:
0
Status:
New User
Location:
Zurich, Switzerland
Twitter:
@HadiGharibi
Last seen:
1 year, 2 months ago
Joined:
1 year, 5 months ago
Email:
h*************@gmail.com

Posts by Hadi Gharibi

<prev • 13 results • page 1 of 2 • next >
0
votes
1
answers
420
views
1
answers
Comment: C: Can featurecounts count number of mapped reads rapidly in arbitrary regions?
... Hi Wei, Code above is the modified version of code I first used with featurecounts. Yes, it is fast enough with 5 cores. I have the latest version of Rsubread. I was not sure whether I was using featurecounts correctly, but with these responses I could modify the code and run it successfully. Thank ...
written 17 months ago by Hadi Gharibi0
0
votes
1
answers
420
views
1
answers
Comment: C: Can featurecounts count number of mapped reads rapidly in arbitrary regions?
... Hi Wei, I could run it more rapidly with more cores thanks to parallel feature in featurecounts. Hadi ...
written 17 months ago by Hadi Gharibi0
3
votes
1
answer
420
views
1
answer
Can featurecounts count number of mapped reads rapidly in arbitrary regions?
... Dear All, I am interested in counting the number of mapped reads in equal size intervals on genome (say 200 bp), my question is whether featurecounts any option for doing this. According to what I have found so far it sounds like it is more appropriate for counting reads mapping to exons, genes, an ...
rsubread featurecounts written 17 months ago by Hadi Gharibi0
0
votes
1
answers
488
views
1
answers
Comment: C: running tximport for salmon quants
... Hey Michael, it is a pleasure, Yes, perfect, it does not give error anymore;)  R CMD build --no-build-vignettes tximport R CMD INSTALL tximport_1.1.3.tar.gz   ...
written 17 months ago by Hadi Gharibi0
0
votes
1
answers
488
views
1
answers
Comment: C: running tximport for salmon quants
... yes it works fine, it gives an error for read_tsv ( Error in reader(x, comment = "#", header = FALSE) : unused argument (header = FALSE) )but it reads all the transcripts. I learned a lot form our conversation:)) ...
written 17 months ago by Hadi Gharibi0
0
votes
1
answers
488
views
1
answers
Comment: C: running tximport for salmon quants
... Thank you so much Michael for the nice conversation :)) ...
written 17 months ago by Hadi Gharibi0
0
votes
1
answers
488
views
1
answers
Comment: C: running tximport for salmon quants
... No, the first transcript does not appear head -3 quant.sf  # salmon (mapping-based) v0.5.1 # [ program ] => salmon  # [ command ] => quant   codes: (in the name of transcripts I omit the rest for readability but it starts from the second transcript) txi.salmon <- tximport(sample_file ...
written 17 months ago by Hadi Gharibi0
0
votes
1
answers
488
views
1
answers
Comment: C: running tximport for salmon quants
... the quant.sf file starts with some information as comments and then the transcripts.(name, length, tpm, number of reads) # salmon (mapping-based) v0.5.1 # [ program ] => salmon  # [ command ] => quant  # [ index ] => { /tcp_idx } # [ libType ] => { SR } # [ unmatedReads ] => { /1.fas ...
written 17 months ago by Hadi Gharibi0
0
votes
1
answers
488
views
1
answers
Comment: C: running tximport for salmon quants
...   Thank you so much, it works now with that option. For the second problem: sf1<- read.delim(sample_files[1], comment ="#") dim(sf1) [1] 119206      4 head(rownames(sf1)) colnames(sf1) [1] "ENST00000335137.3.ENSG00000186092.4.OTTHUMG00000001094.1.OTTHUMT00000003223.1.OR4F5.001.OR4F5.918.CDS.1.9 ...
written 17 months ago by Hadi Gharibi0
0
votes
1
answers
488
views
1
answers
Comment: C: running tximport for salmon quants
... Dear Micheal, previously transcript names had the dots but I removed it now, and still it gives empty vector.(I use it without txOut=TRUE for gene level). mcols(tx)[,"transcript_id"] <- sapply(strsplit(mcols(tx)[,"transcript_id"],"\\."),.subset,1)  txi.salmon <- tximport(sample_files, type ...
written 17 months ago by Hadi Gharibi0

Latest awards to Hadi Gharibi

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 382 users visited in the last hour