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Forum: Bioinformatics 03-17-2017, 10:40 AM
Replies: 7
Views: 4,398
Posted By PeatMaster
Thanks so much to the two of you. This looks to...

Thanks so much to the two of you. This looks to be exactly what I want. I will be sure to verify the output. This will open up a whole new swath of tools for me to use.

Thanks
Forum: Bioinformatics 03-03-2017, 09:55 AM
Replies: 7
Views: 4,398
Posted By PeatMaster
Not back into the read, back into the header line

Hi, my goal is not to put them back into the sequences themselves but to put them at the end of the header line for each sequence in the fastq. Let me know if this is not clear and I can cut and...
Forum: Bioinformatics 03-03-2017, 06:58 AM
Replies: 7
Views: 4,398
Posted By PeatMaster
Adding barcode indexes back into FASTQ headers?

Hi,

I have a set of fastq files from a fungal ITS2 amplicon run on a MiSeq. There are 3 corresponding fastq files: Read1, Read2 and an Index file. In the past, I have worked with fastq files...
Forum: Illumina/Solexa 04-15-2016, 09:49 AM
Replies: 1
Views: 2,227
Posted By PeatMaster
Any input?

Hi, I'm curious if anyone has any input on the post I made a couple weeks ago. I would be grateful for some advice.

To clarify my main questions:

1) What is the best way to remove primers using...
Forum: Illumina/Solexa 04-01-2016, 11:28 AM
Replies: 1
Views: 2,227
Posted By PeatMaster
BBDuk primer trimming on MiSeq 16S data_primers with deletion errors not trimmed

Hi,

I am trying to figure out the best way to trim primers from MiSeq 16S amplicon data with BBduk. I have already filtered phix and trimmed adapters when the fastq file was interleaved. Then I...
Forum: Illumina/Solexa 04-01-2016, 11:18 AM
Replies: 4
Views: 3,335
Posted By PeatMaster
Thanks

OK, I see. Thanks for the help.
Forum: Illumina/Solexa 03-28-2016, 12:26 PM
Replies: 4
Views: 3,335
Posted By PeatMaster
GenoMax, thanks for the reply. The adapter...

GenoMax, thanks for the reply. The adapter trimming on the 3' end makes sense to me now. Thanks.

What I mean by the primer pads are best shown in the the supplement from Tremblay et al. 2015 (see...
Forum: Illumina/Solexa 03-28-2016, 09:14 AM
Replies: 4
Views: 3,335
Posted By PeatMaster
Adapter trimming with BBduk

Hi, I am working with some MiSeq 16S and ITS2 amplicon sequence data generated by JGI. Previously I utilized the data after it was quality controlled and merged but now I am going back to the...
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