SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Smatools mpileup thinks my sorted bam files are not sorted plumb_r Bioinformatics 6 04-28-2014 08:22 AM
convert sorted bam to sorted sam for htseq-count ugolino Bioinformatics 3 10-19-2012 06:30 AM
RPKM and read counts from RNA-seq rakesh12 Bioinformatics 1 06-28-2012 08:58 AM
RNA SEQ Data read counts from known and unknown regions deveci Bioinformatics 0 06-24-2011 02:33 PM
Tag counts for RNA seq experiment sanush SOLiD 3 12-03-2009 07:37 AM

Reply
 
Thread Tools
Old 06-11-2013, 05:54 AM   #1
SandhyaKiran
Junior Member
 
Location: india

Join Date: Jun 2013
Posts: 1
Default RNA Seq counts on sorted data

I am using htseq-count to get gene counts from paired-end illumina data. Alignment was done by tophat.

When I used accepted_hits.bam after sorting the bam file with default option of sort by position

samtools sort accepted_hits.bam accepted_hits_test &
samtools view accepted_hits_test.bam | htseq-count --mode=intersection-nonempty - genes.gtf > genecounts1.txt

I got warnings - 'Is SAM properly sorted?'. But I got gene counts.


When I sorted BAM file with sort -n option and run htseq-count for gene counts, using the following commands, I didn't get any warnings except about the non-availability of information on Chr M in gtf file.

samtools sort -n accepted_hits.bam accepted_hits_sortedN &
samtools view accepted_hits_sortedN.bam | htseq-count --mode=intersection-nonempty - genes.gtf > genecounts2.txt


Counts obtained in both the ways were different. Counts in genecounts1.txt are aproximately half to the counts obtained in genecounts2.txt. And, counts obtained form Cufflinks are matching with genecounts1.txt (sort by position)

Which one should I rely on - genecounts1 ? or genecounts2 ?


Thanks,
Sandhya
SandhyaKiran is offline   Reply With Quote
Reply

Tags
rna-seq counts

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:25 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO