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Forum: Introductions 09-21-2015, 01:32 PM
Replies: 9
Views: 2,687
Posted By mcarson
Brian, a couple final questions. I know the...

Brian, a couple final questions. I know the "normal" JGI pipeline uses PANDAseq to merge reads so I assume BBMap is used to adapter trim and quality filter. However it seems like your bbmerge is...
Forum: Introductions 09-20-2015, 01:13 PM
Replies: 9
Views: 2,687
Posted By mcarson
Brian thanks for the info. Do you happen to know...

Brian thanks for the info. Do you happen to know of any online courses or lectures that cover these topics in more detail? I've been thrown into the bioinformatics realm and a big part of the...
Forum: Introductions 09-19-2015, 12:58 PM
Replies: 9
Views: 2,687
Posted By mcarson
Thanks for the suggestions, and I'm pretty...

Thanks for the suggestions, and I'm pretty confident in the reverse read primer as I get tens of thousands of hits when I search the different variants in a text file. I'll look into BBMap, are there...
Forum: Introductions 09-19-2015, 09:52 AM
Replies: 9
Views: 2,687
Posted By mcarson
@MISEQ06:359:000000000-AEFPR:1:1101:16407:1545...

@MISEQ06:359:000000000-AEFPR:1:1101:16407:1545 1:N:0:ACATCTTGACG...
Forum: Introductions 09-19-2015, 08:51 AM
Replies: 9
Views: 2,687
Posted By mcarson
Hello and JGI problems

Hello, totally new to the forum and somewhat new to the sequencing world. I've dealt with miseq data before when it arrives in the "standard" forward/reverse fastq reads with or without primers. I...
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