Difference between TopHat and PASS

[charlie_sequencing]

Hi folks, I am a newcomer to NGS data analysis. I read two papers regarding the application of TopHat and PASS respectively to carry out NGS reads mapping to reference genome. Has anyone had any experiences dealing with those two programs? Which one might be a better choice to use when trying to map Illumina reads to reference genome to identify mismatches? Any option in TopHat to implement in order to record the mismatch coordinates?

Thanks!

[samanta]

Hi folks, I am a newcomer to NGS data analysis. I read two papers regarding the application of TopHat and PASS respectively to carry out NGS reads mapping to reference genome. Has anyone had any experiences dealing with those two programs? Which one might be a better choice to use when trying to map Illumina reads to reference genome to identify mismatches? Any option in TopHat to implement in order to record the mismatch coordinates?

Thanks!

What kind of data? Transcriptome?

[charlie_sequencing]

Illumina data, around 75 bp per read. Any suggestions on that, samanta? Thanks!

[samanta]

You still did not say whether it is transcriptome (RNA-seq) data, or just resequencing of genome for SNP comparison.

If you have genomic data, you can use Bowtie (part of Tophat pipeline) and map reads to the genome. If you get the data output in SAM format, samtools can be used to get mismatches.

If you have RNA data, Tophat+Bowtie can be used together in mapping. Tophat helps in mapping of splice junctions.

I have not tried PASS, but I believe Tophat, Bowtie and samtools have much larger community.

[charlie_sequencing]

Thanks so much, samanta! Yeah, I am using RAN-Seq data.

Is there any option that I can use in tophat to output the mismatch information for each read that has been mapped back to the reference genome?

[samanta]

Not that I know of. Tophat runs Bowtie to do its alignments, and Bowtie produces mismatches. However, to get a nice list of SNPs etc, you need to ask Bowtie to print output in SAM format and then try samtools. It is very easy. Bowtie manual has an example about how to do it.

[charlie_sequencing]

Great! I'll check that manual. Thanks so much for your help!