multiqc for htseq output

1

Hi,
Is it posible to do a Multiqc after htseq? However as the htseq output does not give information about the percentage of aligned reads (shows ony the number of no_features, ambiguous, too low aQual ,not aligned and not unique alignment) how is it possible? I have done Multiqc using featureCounts, but not what the input should be when i use the htseq data

Thanks,G

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2

Hi @GGOPA
yes, MultiQC can visualize summary files from htseq-count. % of alignments can be calculated from numbers in summary files. Note that htseq-count summaries describe alignments, not reads, eg a read mapped to two locations has two alignments.
Hope this answers the question.
Kind regards,
Igor

3

Thanks, Igor.

I get 2 output files for htseq. One that shows the counts (Gene ID and number of aligned reads) and another that says (no feature) with details of ‘ambiguous, low_aQual, non-aligned and not-unique aligned’ as shown in my previous post. I do not see a file called ‘Summary’ as the one that is generated by featureCounts. And Multiqc could not be executed by with these two files.
Many thanks,
GG

4

Hi @GGOPA
I am sorry for clumsy explanation. Summary file is one with (no feature) at the end. It contain summary for alignment counting. During setup of MultiQC job select HTSeq for Which tool was used generate logs?. Select only summary files with (no feature). Do not use count files.
Hope it helps.
Kind regards,
Igor