Question: Question: Error HISAT2 output for HTseq-count
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gravatar for 11yj3312
4 days ago by
11yj33120
11yj33120 wrote:

Dear all, I am analyzing paired-end stranded RNAseq data . I would be interested in using HISAT2 for the alignment, and HTseq-count to count the features of the aligned reads. When I used HTseq-count to count the reads:

htseq-count -r pos -f bam SRR3589957_sorted.bam ../reference/gencode.v26lift37.annotation.gtf > SRR3589956.count

However,I got this error :

Error occured when processing SAM input (record #69114540 in file SRR3589957_sorted.bam): my_showwarning() takes from 3 to 5 positional arguments but 6 were given [Exception type: TypeError, raised in warnings.py:99]

I converted sam file to bam and sorted the reads by pos using samtools

Does anyone has an idea of the problem with the reads aligned with HISAT2? Are they compatible with HTseq-count?

Thank you very much for any help. Jing Yu

ADD COMMENTlink modified 4 days ago • written 4 days ago by 11yj33120

Not an answer to your question, but consider featureCounts which is an ultra fast read count program and work well with Hisat2 output SAM file. Also, it rearrange read itself and final table of read count matrix for all paired end SAM can be obtained. For ex,

featureCounts -p -t exon -g gene_id -a genes.gtf -o counts.txt  con1.sam con2.sam treat1.sam treat2.sam
ADD REPLYlink modified 4 days ago • written 4 days ago by anc.informatics0

Think you !I will try it

ADD REPLYlink written 4 days ago by 11yj33120

That's an odd warning, are you using the latest htseq-count version?

But as said by anc.informatics: featureCounts is an excellent choice.

ADD REPLYlink written 4 days ago by WouterDeCoster24k

I have tried the latest htseq-count,No previous error occurred.Think you!

ADD REPLYlink written 3 days ago by 11yj33120
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