Question: Getting average fragment length for single end reads
0
gravatar for Sreeraj Thamban
5 months ago by
Indian Institute of Science Education and Research
Sreeraj Thamban30 wrote:

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

ADD COMMENTlink modified 5 months ago by Buffo480 • written 5 months ago by Sreeraj Thamban30

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?

ADD REPLYlink written 5 months ago by James Ashmore2.1k

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.

ADD REPLYlink written 5 months ago by Sreeraj Thamban30
2
gravatar for Buffo
5 months ago by
Buffo480
Buffo480 wrote:

Prinseq and biopieces mainly

ADD COMMENTlink written 5 months ago by Buffo480

Thank you , i will try these two

ADD REPLYlink written 5 months ago by Sreeraj Thamban30

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

ADD REPLYlink written 5 days ago by Thomas80
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