Hi all,
In RNA-seq studies , how can I get the info needed for the calculation of "Mean Inner Distance between Mate Pairs" which is a parameter needed by Tophat?
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english.server
I'd generally align to the transcriptome using bowtie2 for each sample, run picard tools (CollectInsertSizeMetrics.jar) on the resulting file. Get the number for MEAN_INSERT_SIZE, then work out MEAN_INSERT_SIZE - (2 x read length)
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andrew.j.skelton73
I'd generally just run BBMap, which does not require that parameter, as it calculates it automatically. Of course, I'm somewhat biased, as I wrote BBMap. But I have yet to find a scenario where Tophat is a desirable program to run over the alternatives (BBMap or STAR).
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Brian Bushnell
Agreed, I have to admit I've never used BBMap, but STAR, and HISAT don't require this parameter - It's usually computed internally.
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andrew.j.skelton73
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Thank you Andrew for your response. I am sorry to ask this but how can I find read length? Is it equal to InsertSize in SRA database?
run the fastq file through fastqc, or look at one of the entries in the fastq and figure out how long the line is, each entry is a single read (plus quality score, header, etc)
Thanks again