Partial alignment of transcripts in PASA

[Chudar Chudar]

Dear Dr. Brain and others,

I am new to PASA. I want to identify the mRNA coverage outside the transcript boundaries in genome. For that I initially used PASA which maps transcriptome to genome using GMAP and BLAT. In my case, my transcriptome was assembled using trinity. I ran the PASA like following

perl ~/PASApipeline-2.0.2/scripts/Launch_PASA_pipeline.pl -c pasa.alignAssembly.Template.txt -C -R -g ../Genome_Assemblies_Fasta/genome.fa -t ../transcriptome.fasta --ALIGNERS blat,gmap --CPU 40 --TRANSDECODER.

As expected, the script ran for while and generated the output with many gtf, gff3 file and bed files.

I am using GTF files form gmap, BLAT to visualize the alignment and coverage in IGV. I found   that only a part of a transcript is aligned while the remaining part is missing. As result, the read coverage region which I found outside transcript boundaries were part of the transcript whose regions were not aligned and not represented in GTF file.

How can I make sure that the complete transcript is aligned so that I can trust the GTF file generated and use it for subsequent analysis.

Kindly guide me

Regards

Chudar

[bh...@broadinstitute.org]

Hi

The gtf file is only going to represent the aligned regions.  The .validations files will contain info on what percentage of the transcript aligned, in case that's helpful.  Finally, pasa assemblies will be based on only those alignments that meet the minimum percent length aligned criteria.

Best,

~b

Sent from my iPad