Any possible method/tool that could refers the number of overlapping sequences used t

[bambus]

HI,

I work with Metatranscriptomics data(sequenced using Illumina technolgy).I did de-novo transcriptome assembly using SOAP-Denovo-Trans assembler and now looking for a tool/software that could help me out to find the total number of overlapped reads involved to form a single contig to understand how good or bad the coverage is.



Any suggestions could be helpful.

Thank you in advance.

[SES]

It is difficult to infer such things from SOAP assemblies since you only get a Fasta file of contigs as a result. One approach would be to map your reads with bwa and try to get coverage with samtools or something similar. This may not give you the exact result since k-mers formed your contigs (not whole reads), but it may be close enough to be informative.

[bambus]

Thank you for the reply.

Do I get better scope if I change the assembler before going with mapping step but,not clear which one to use for Meta-transcriptomics data.

Could you suggest me a better tool for assembling.

[SES]

Thank you for the reply.

Do I get better scope if I change the assembler before going with mapping step but,not clear which one to use for Meta-transcriptomics data.

Could you suggest me a better tool for assembling.

Sorry for the delay. You may want to consider MetaVelvet for assembling. I know you can track the reads that go into each contig with Velvet, so you may be able to do the same with MetaVelvet.