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Old 12-10-2013, 02:15 PM   #1
bambus
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Default Any possible method/tool that could refers the number of overlapping sequences used t

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.
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Old 12-12-2013, 07:15 AM   #2
SES
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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.
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Old 12-17-2013, 01:50 AM   #3
bambus
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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.
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Old 12-18-2013, 09:39 AM   #4
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Quote:
Originally Posted by bambus View Post
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.
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