Question: Tophat's Mean Inner Distance between Mate Pairs
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gravatar for english.server
4.7 years ago by
Germany
english.server210 wrote:

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?

rna seq tophat • 2.5k views
ADD COMMENTlink modified 4.7 years ago by Brian Bushnell17k • written 4.7 years ago by english.server210
1

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?

ADD REPLYlink written 4.7 years ago by english.server210

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)

ADD REPLYlink written 4.7 years ago by andrew.j.skelton736.0k

Thanks again

ADD REPLYlink modified 7 months ago by RamRS27k • written 4.7 years ago by english.server210
2
gravatar for andrew.j.skelton73
4.7 years ago by
London
andrew.j.skelton736.0k wrote:

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)

ADD COMMENTlink modified 7 months ago by RamRS27k • written 4.7 years ago by andrew.j.skelton736.0k
1
gravatar for Brian Bushnell
4.7 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

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).

ADD COMMENTlink modified 7 months ago by RamRS27k • written 4.7 years ago by Brian Bushnell17k

Agreed, I have to admit I've never used BBMap, but STAR, and HISAT don't require this parameter - It's usually computed internally.

ADD REPLYlink modified 7 months ago by RamRS27k • written 4.7 years ago by andrew.j.skelton736.0k
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