Question: Getting average fragment length for single end reads
0
gravatar for Sreeraj Thamban
14 months ago by
Indian Institute of Science Education and Research
Sreeraj Thamban90 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 8 weeks ago by dark.lord0 • written 14 months ago by Sreeraj Thamban90
2

Prinseq and biopieces mainly

ADD REPLYlink written 14 months ago by Buffo1.1k
1

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 9 months ago by Thomas90

Thank you , i will try these two

ADD REPLYlink written 14 months ago by Sreeraj Thamban90

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

ADD REPLYlink written 8 weeks ago by dark.lord0

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.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by genomax52k
1
gravatar for James Ashmore
14 months ago by
James Ashmore2.5k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.5k wrote:

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 COMMENTlink written 14 months ago by James Ashmore2.5k

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 14 months ago by Sreeraj Thamban90
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