Question: Which Snp Caller / Method To Use After Aligning Rna-Seq With Tophat
1
gravatar for William
6.4 years ago by
William4.5k
Europe
William4.5k wrote:

Which SNP caller / method can / should I use after aligning RNA-seq data with TopHat?

For genomic data I use GATK, but supposedly it is not just as easy as running GATK on the TopHat RNA-seq data. The team from Broad has no information / documentation on how to use GATK for RNA-seq data.

I don't have any variants yet from DNA re-sequencing.

tophat2 snp rna-seq • 3.2k views
ADD COMMENTlink modified 5.5 years ago by jockbanan380 • written 6.4 years ago by William4.5k
1
gravatar for Chris Miller
6.3 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

VarScan will happily make calls on RNAseq data with a matched normal (from RNAseq or exome). Be sure to consider all of the parameters carefully, especially minimum coverage levels and such.

ADD COMMENTlink written 6.3 years ago by Chris Miller21k

Do you have some advices for strand-specific RNA-Seq (2x50bp) ?

ADD REPLYlink written 6.3 years ago by Nicolas Rosewick8.1k

Don't have a lot of experience with this, but some tools have steps with a directional filter (variants only appearing in one strand are removed as artifacts). Make sure that any such option is off.

ADD REPLYlink written 6.3 years ago by Chris Miller21k
0
gravatar for yyaobo
6.4 years ago by
yyaobo30
United Kingdom
yyaobo30 wrote:

I haven't looked at GATK on RNA-seq data, instead I used samtools/BCFtools, it's probably not the best, but it will get you started.

ADD COMMENTlink written 6.4 years ago by yyaobo30
0
gravatar for jockbanan
5.5 years ago by
jockbanan380
Czech Republic
jockbanan380 wrote:

Current GATK (2.8-1) seems not to be a good option for reads mapped with TopHat (and any other splice-aware aligners). When running on .bam file generated by TopHat, you end up with an error saying you should remove (or ignore) all reads with 'N' cigar string (spliced reads). You can force GATK to process these reads, but the authors say that this may result in something not really meaningful.

ADD COMMENTlink written 5.5 years ago by jockbanan380
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