Hi everyone, I am new with Velvet and I have some questions regarding velvetg parameters.
I am doing the de novo assembly for my Illumia...
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velvetg coverage parameter
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tophat2 some parameters are not working (--no-novel-indels and -a)
I used tophat2 to map reads with --no-novel-indels and -a 6 parameters. Once the mapping is done, I examined the result (accepted_hits.bam) and found...Last edited by statsteam; 05-28-2014, 03:48 PM. Reason: putting a correct example for anchor length <6 -
blastall blastx filter different hits on one contig
Dear all,
I performed a blastx of some thousand contigs of size between 1500 and 5000 bp against uniref-protein database. To speed it up... -
Tophat2 "joining segment hits" does not complete
Tophat2 runs nicely (6 hours) up to the step "joining segment hits". But this step (single core process, named "long_spanning_reads")...Last edited by Sniwells; 10-17-2012, 11:20 AM. -
BFast match and preprocess questions
Hi,
I am trying to map solid reads using bfast, and have several questions on using it, any help will be highly appreciated!
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Set ssaha2 parameter for mismatch
I want to align 454 reads against a transcriptome reference using sssaha2. Tolerance are set to five mismatchs for each alignment. Which parameter can... -
maq with no mismatches
Hello,
Is it possible to run maq to allow no mismatches in the alignment? I tried using -n but that doesn't seem to allow 0 as a value....
