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Getting average fragment length for single end reads

Hi, I have a set of raw files of RNASeq single end reads. Is there any tool for getting the average fragment length and SD from these files? I don't have access to a Bioanalyzer. I wanted to run Kallisto for these files. Thank you

rna-seq kallisto differential expresion
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updated by dark.lord • dark.lord • written by Sreeraj Thamban Sreeraj Thamban

Hello,

If I am not mistaken, these two pieces of software will give you statistics relating to reads and not fragments?

Which although useful, it is not what is requested by kallisto

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written by Thomas Thomas

There is no way to calculate average fragment size based on single-end sequencing data. You may be able to get a rough estimate based on Bioanalyzer/Tapestation results for the library that was sequenced.

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written by GenoMax GenoMax

Is this not what MACS2 accomplishes using its sliding window approach?

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written by millerh1 • millerh1

1 answer

If you have single-end reads and don't have the Bioanalyzer output there is no way to calculate the actual fragment length. Instead just use a predicted value typical of most sequencing machines, say ~200bp?

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written by James Ashmore James Ashmore

Hi I used 150-200bp (best guess) as average fragment length in Kallisto but when I tried to reproduce the result from a tophat-cufflinks-cuffdiff pipeline the results shows very significant variation, but for paired-end reads, it was very consistent. So I think giving accurate fragment length is vital in Kallisto.

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written by Sreeraj Thamban Sreeraj Thamban

Hi Sreeraj I am having the same problem now, Did you find a solution please?

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written by ayaosama2111 • ayaosama2111

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