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Question: Getting average fragment length for single end reads
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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 2.7 years ago Sreeraj Thamban • 140 • updated 21 months ago dark.lord • 0
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Prinseq and biopieces mainly

ADD REPLYlink 2.7 years ago
Buffo
♦ 1.6k
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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 2.3 years ago
Thomas Bradley
• 90
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Thank you , i will try these two

ADD REPLYlink 2.7 years ago
Sreeraj Thamban
• 140
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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 21 months ago
dark.lord
• 0
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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 21 months ago
genomax
68k
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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 2.7 years ago James Ashmore ♦ 2.6k
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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 2.7 years ago
Sreeraj Thamban
• 140

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