Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
htseq-count paolo.kunder Bioinformatics 10 10-22-2014 04:45 AM
htseq-count low count problem gandalf886 Bioinformatics 3 08-23-2014 07:05 AM
HTseq-count of zero halffedelf RNA Sequencing 14 04-17-2014 10:31 AM
Which ID should be used for HTSeq-count? syintel87 Bioinformatics 11 02-07-2013 12:16 AM
multiBamCov or htseq-count to count read per feature ? NicoBxl Bioinformatics 1 07-03-2012 02:05 AM

Thread Tools
Old 11-15-2014, 03:42 PM   #1
Junior Member
Location: USA

Join Date: Nov 2014
Posts: 1
Default htseq-count

Hello All,

I have some .bam files from samples of human, two group of sample: First one for Normal and the other for patient, I have no access for the reads files. and i want to generated the genes counts to use it with in edgeR. i am new to these things. Could any one please help me with the steps.
i directly tied the following command after i install the htseq-count

htseq-count -f .bam .gtf > counts.txt

from where i can get the the right .gtf file to use and do i need to put all the .bam files of every group together to get the counts.

Please help
moon_ligth is offline   Reply With Quote
Old 11-15-2014, 04:18 PM   #2
Senior Member
Location: Montreal

Join Date: May 2013
Posts: 367

Start by checking the header of one of the BAM files.
samtools view -H name.bam

At the end of the header section, check the data field CL (command line) in the PG (Program) line.
This will provide you with useful information about the GTF file to use, e.g. Ensembl or UCSC.
blancha is offline   Reply With Quote
Old 11-15-2014, 04:26 PM   #3
Senior Member
Location: Montreal

Join Date: May 2013
Posts: 367

For your second question, no you shouldn't merge the BAM files together if each BAM file corresponds to one sample.

You will count the reads for each BAM file separately.
DESeq2 will take as input the htseq-count for each file.

Incidentally, if you are not able to identify the exact GTF file used from the header, you could always extract the reads from the BAM file and repeat the alignments. This would be more work however, and not absolutely necessary.
blancha is offline   Reply With Quote

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 10:09 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO