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Forum: Bioinformatics 07-10-2020, 07:06 PM
Replies: 109
Views: 38,357
Posted By phylloxera
Looks like everything went fine after I...

Looks like everything went fine after I 'unwrapped' the input fasta.
Forum: Bioinformatics 07-09-2020, 02:15 PM
Replies: 109
Views: 38,357
Posted By phylloxera
Hi, I've been using clumpify for sometime now....

Hi, I've been using clumpify for sometime now. Thanks!
Seem to have encountered a strange and unexpected result.
pigz -dc test.fna.gz | grep "^>" | wc -l #4149
~/bbmap/clumpify.sh in=test.fna.gz...
Forum: Bioinformatics 01-10-2018, 01:31 PM
Replies: 244
Views: 113,097
Posted By phylloxera
Ultimately, i'd like to do variant calling on a...

Ultimately, i'd like to do variant calling on a combined pac bio / illumina whole viral genome dataset. I am working with BBMap right now as it has the intuitive minid flag, which seems desirable. As...
Forum: Bioinformatics 05-18-2017, 07:06 AM
Replies: 335
Views: 158,506
Posted By phylloxera
re: different results from command line and geneious plugin

Yes, the adapters files are different. Geneious says using All Truseq, Nextera, and PhiX adapters (152) sequences. The count in the resources folder of bbmap is 154 sequences. I don't know which 2...
Forum: Bioinformatics 05-17-2017, 01:46 PM
Replies: 335
Views: 158,506
Posted By phylloxera
Getting different results with bbduk command line vs geneious plugin

Hi,

I have been searching the default settings in the command line and still haven't identified the source of the discrepancy... Here is my linux command:

sh ~/bbmap/bbduk.sh...
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