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How to find out the insert size in RNA seq data
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14 months ago
rj.rezwan • 0

Hi,

please tell me according to the following shared red circle in picture, can we say this as a insert size of our RNA-seq data.[1]: https://ibb.co/jf4keF

RNA-Seq • 2.3k views
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As Chris suggested, you need to align your reads to get a SAM/BAM file and then run 'samtools stats' to get information about insert sizes..it will also give you an insert size distribution graph..

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14 months ago
ivivek_ngs ♦ 4.8k
Seattle,WA, USA

The easiest way to find it programmatically is to convert the SRA to fastq on the fly (if you are unable to get it from their documents) and proceed with alignment to produce the bam file. After that just use bamtools with the below command and it will give the average and the median insert size. Good luck!

bamtools stats -i foo.bam -insert
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15 months ago
Chris Fields ♦ 2.1k
University of Illinois Urbana-Champaign

No, that's the run ID, see the wikipedia article. If you have paired-end reads, you'll need to align them as such for an insert size to be reported.

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14 months ago

If the data comes from SRA database, then you can search that info there. If it is a newly sequenced data, than maybe easiest would be to ask sequencing provider.

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2.1 years ago
Michi • 950
Barcelona

also samtools has a very similar command to bamtools:

samtools stats --insert-size foo.bam

you can additionally speed upt the process by using --threads 10

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