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Forum: Bioinformatics 01-12-2015, 08:47 PM
Replies: 6
Views: 1,752
Posted By arkilis
Finally I used the command you suggested: ...

Finally I used the command you suggested:

bbsplit.sh in1=read1.fastq in2=read2.fastq ref=KIR_nuc.fasta outu1=no_match_1.fq outu2=no_match_2.fq outm1=matched_to_KIR1.fq outm2=matched_to_KIR2.fq
...
Forum: Bioinformatics 01-11-2015, 04:19 PM
Replies: 6
Views: 1,752
Posted By arkilis
Sorry for the confusion. KIR gene from...

Sorry for the confusion.

KIR gene from www.ebi.ac.uk/ipd/kir in fasta format. I might want to use this as the database to find out how many of them are in the current sequence files. I read some...
Forum: Bioinformatics 01-11-2015, 03:04 PM
Replies: 6
Views: 1,752
Posted By arkilis
Thanks GenoMax. I tried the whole weekend....

Thanks GenoMax.

I tried the whole weekend. BBSplit/BBMap looks like a alignment tool. I have the KIR gene database, need to get the what it has (KIR) in the sequence files. Any clue on this?
...
Forum: Bioinformatics 01-08-2015, 04:41 PM
Replies: 6
Views: 1,752
Posted By arkilis
how to use mafft do find out kir genes?

recently get a batch of data from miseq, is there way to use mafft to find those kir genes?

I searched online for mafft usage, which looks no where to put kir databases.
...
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