Question: Read length from HT-Seq
gravatar for gupta
2.4 years ago by
gupta30 wrote:


Sorry for asking this very basic question. I have paired-end RNA-Seq data. After initial adapter and quality trimming, I used Tophat for alignment. Later, I obtained the read count using HT-Seq from the alignment file.

My questions is: Can I also somehow obtain the length of the reads that were counted/filtered by HT-Seq? This would allow me to see the distribution of read length in the data.

Thanks in advance for any help.

Best, Pooja

ht-seq rna-seq • 683 views
ADD COMMENTlink modified 2.4 years ago by Jennifer Hillman Jackson25k • written 2.4 years ago by gupta30
gravatar for Jennifer Hillman Jackson
2.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello Pooja,

The htseq_count tool form option "Additional BAM Output" can be used to produce a dataset that can be parsed for both feature and read length. Search for the keyword "bam" in the tool panel to review the tools to perform the summary (are several choices). Or, convert the BAM-to-SAM, then parse the SAM file as a tabular dataset.

Hopefully this helps! Jen, Galaxy team

ADD COMMENTlink written 2.4 years ago by Jennifer Hillman Jackson25k

Thank you so much Jen. Its really helpful :)

ADD REPLYlink written 2.4 years ago by gupta30
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