Hello.
I am interested in removing false positives from an RNAseq experiment using an aligner Tophat parameter
--insertions/--deletions <.juncs file>
Supply TopHat with a list of insertions or deletions with respect to the reference. Indels are specified one per line, in a tab-delimited format, identical to that of junctions. Records look like:
I am supposing I would get the dbSNP file from the database.
Advice for those who have used this parameter for alignments?
I am interested in minimizing false positives from the alignment.
there are two ways to achieve validation of your data
1) use different software to get similar comparisons
2) supply a more accurate pipeline.
As of now, I use trimming software to remove the adapters, and align the complete fastq file to the reference. But if there are large indels/deletions this could be problematic.
Thank you in advance
I am interested in removing false positives from an RNAseq experiment using an aligner Tophat parameter
--insertions/--deletions <.juncs file>
Supply TopHat with a list of insertions or deletions with respect to the reference. Indels are specified one per line, in a tab-delimited format, identical to that of junctions. Records look like:
I am supposing I would get the dbSNP file from the database.
Advice for those who have used this parameter for alignments?
I am interested in minimizing false positives from the alignment.
there are two ways to achieve validation of your data
1) use different software to get similar comparisons
2) supply a more accurate pipeline.
As of now, I use trimming software to remove the adapters, and align the complete fastq file to the reference. But if there are large indels/deletions this could be problematic.
Thank you in advance