Question: Get bowtie2 to ignore isoform variants from Trinity assembly?
0
gravatar for CephBirk
11 months ago by
CephBirk0
Woods Hole, MA, USA
CephBirk0 wrote:

So I've run bowtie2 against my Trinity assembly and get a high proportion of paired end reads that align concordantly at more than one place. I am suspicious that they're aligning to multiple isoform variants all from the same "gene" group.

Fortunately, I've got a Trinity assembly that also includes a gene_trans_map that identifies which isoforms belong with which "gene" grouping.

How can I get bowtie2 to ignore isoform variants with a given "gene" group (defined by gene_trans_map) when it calculates the percent of reads that concordantly align exactly once or more than one time? I haven't been able to find anything like this in the help page but I would suspect this may be a common thing people want to do... I would prefer not to have to use the -a parameter given how much this slows things down.

rna-seq • 224 views
ADD COMMENTlink modified 11 months ago by h.mon29k • written 11 months ago by CephBirk0
2
gravatar for h.mon
11 months ago by
h.mon29k
Brazil
h.mon29k wrote:

Try collapsing the trascriptome assembly into supertranscripts, this should alleviate the multi-mapping problem. See the Trinity documention on SuperTranscripts.

ADD COMMENTlink written 11 months ago by h.mon29k

Thanks! This is just what I was looking for and does shift about 20% of my reads from the "aligned concordantly >1 times" category to the "exactly one time" category.

ADD REPLYlink written 11 months ago by CephBirk0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1023 users visited in the last hour