SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
DEXSeq Using Counts File From htseq-count FuzzyCoder Bioinformatics 20 01-03-2016 11:18 PM
IGV sees many counts, but HTSeq-count counts 0 snownontrace Bioinformatics 12 08-27-2015 04:22 AM
Zero counts in htseq-count output lanner Bioinformatics 2 05-05-2014 12:36 AM
htseq-count only not-unique counts moser Bioinformatics 7 08-09-2013 08:28 AM
htseq-count : 0 counts per miRNA JPerales RNA Sequencing 4 06-04-2013 06:00 AM

Reply
 
Thread Tools
Old 01-15-2016, 05:11 AM   #1
super0925
Senior Member
 
Location: UK

Join Date: Feb 2014
Posts: 206
Default RNA-Seq: GFOLD counts is different from HTSeq-count

Does anybody use GFOLD before?
http://compbio.tongji.edu.cn/~fengjx/GFOLD/gfold.html

Why do I use these two tools count reads but give different results?

In GFOLD manual, “Because of possible overlapping of multiple genes, a read could be mapped to the overlaped region of multiple genes. In this case, a read is counted multiple times with each time for each gene. Furthermore, if a gene is on multiple chromosomes or different strands of the same chromosome, only exons on one strand of one chromosome (the one appear first in the annotation file) will be assigned to this gene. Exons not on this strand of the chromosome will be discarded.”

Code:
gfold count -ann genes.gtf -tag sample1.sam -o sample1.read_cnt

htseq-count --minaqual=10 --mode union sample1.sam genes.gtf>htseq.counts
Is that because HTSeq skip the alignment quality lower reads?
super0925 is offline   Reply With Quote
Old 01-15-2016, 05:28 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

The part you showed from the GFOLD manual is completely different from what htseq-count and featureCounts do, so it's expected that you'd get different results.
dpryan is offline   Reply With Quote
Reply

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 07:45 AM.


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