Getting average fragment length for single end reads

Question

[Sreeraj Thamban]

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

[Buffo]

Prinseq and biopieces mainly

[Thomas]

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

[Sreeraj Thamban]

Thank you , i will try these two

[dark.lord]

Is it wrong to use the one-liner provided here to calculate average fragment size and sd? Question: Mean and SD read length from a range of fastq files

[GenoMax]

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.

[millerh1]

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

Answer 1

[James Ashmore]

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?

[Sreeraj Thamban]

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.

[ayaosama2111]

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