Question: Tophat's Mean Inner Distance between Mate Pairs
0
gravatar for english.server
3.8 years ago by
Germany
english.server160 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 • 2.2k views
ADD COMMENTlink modified 3.8 years ago by Brian Bushnell16k • written 3.8 years ago by english.server160
2
gravatar for andrew.j.skelton73
3.8 years ago by
London
andrew.j.skelton735.8k 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 written 3.8 years ago by andrew.j.skelton735.8k
1
gravatar for english.server
3.8 years ago by
Germany
english.server160 wrote:

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 COMMENTlink written 3.8 years ago by english.server160

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 3.8 years ago by andrew.j.skelton735.8k

Thanks again

 

ADD REPLYlink written 3.8 years ago by english.server160
1
gravatar for Brian Bushnell
3.8 years ago by
Walnut Creek, USA
Brian Bushnell16k 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 written 3.8 years ago by Brian Bushnell16k

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 written 3.8 years ago by andrew.j.skelton735.8k
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