Hej!
I am working on a data my group received from MWG. They were using, as far as I know 454 sequencing to sequence short 3' fragments of cDNA from two populations. My task is to assemble the data and compare the abundance of the transcript.
I am a beginner, so please excuse me if my questions are silly, here they are:
1. I have fasta and quality files. I feed them to phrap and I am getting an output - so far so good. Now, how can I obtain information on what was merged into the resulting contigs? I need this information to make comparison of transcript abundance. Phrap provides me with a huge report file but I am not sure how to find this information. Ideally I want to automate the process using python scripts - that is run assembly in phrap and parse the output so I can have a table with a contig sequence and number of reads that were used to create it.
2. Is this even possible? Should I perhaps use some other tools?
Thanks in advance.
Best regards
Marian Plaszczyca
I am working on a data my group received from MWG. They were using, as far as I know 454 sequencing to sequence short 3' fragments of cDNA from two populations. My task is to assemble the data and compare the abundance of the transcript.
I am a beginner, so please excuse me if my questions are silly, here they are:
1. I have fasta and quality files. I feed them to phrap and I am getting an output - so far so good. Now, how can I obtain information on what was merged into the resulting contigs? I need this information to make comparison of transcript abundance. Phrap provides me with a huge report file but I am not sure how to find this information. Ideally I want to automate the process using python scripts - that is run assembly in phrap and parse the output so I can have a table with a contig sequence and number of reads that were used to create it.
2. Is this even possible? Should I perhaps use some other tools?
Thanks in advance.
Best regards
Marian Plaszczyca
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