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Htseq Count Sam

Hi everyone

I want to use htseq-count to count the number of reads for the features i have but htseq-count says:

If you have paired-end data, you have to sort the SAM file by read name first.

How can i do that if i don't want to use msort.

Regards V

htseq counts
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updated by Irsan Irsan • written by Varun Gupta Varun Gupta

3 answers

Use samtools for sorting: samtools sort -n file.bam filesortedbyreadname

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written by Linxe • Linxe

Does 'samtools sort -n' properly handle paired end data with multiple alignments per read (e.g. rna-seq reads aligned by TopHat)?

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written by Malachi Griffith Malachi Griffith

Hi Malachi, i am having exactly the same problem. Did you sort out how to deal with this?

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written by roll roll

For htseq-count it won't actually matter as multimapping reads will be ignored in any case (htseq-count looks at the NH:i: auxiliary tag).

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written by Devon Ryan Devon Ryan

You have mentioned that SAM file has to be sorted but in the answer you have mentioned a BAM file. ??? Is that a TYPO ???

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written by venks venks

You can also use SortSam.jar from picardtools

java -jar /path_to_folder_picardtools/SortSam.jar INPUT=yourfile.sam OUTPUT=readSorted.sam SORT_ORDER=queryname VALIDATION_STRINGENCY=lenient
• 263 views • link
written by Irsan Irsan

I have the same question, I have sorted the .bam file and convert it to .sam file : didnt work for ht seq, then I have sorted the .sam file and given for ht seq, didnt work..!! Do you have any other suggestions for sorting the sam file (paired end data) by read name?

• 0 views • link
written by sethugunja • sethugunja

Firstly, try starting a new thread rather than just answering an almost year-old question with another question. Secondly, we can't help you if you just says "does not work" without providing any details. We're good, but we don't read minds.

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written by Devon Ryan Devon Ryan

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