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Forum: Genomic Resequencing 02-19-2017, 09:38 AM
Replies: 8
Views: 1,799
Posted By AgatheJ
Thanks again for your answer! I have removed...

Thanks again for your answer!

I have removed Illumina adaptors because we used them for multiplexing. What we did is to prepare DNA libraries using a NebNext Library prep kit and in-house...
Forum: Genomic Resequencing 02-13-2017, 08:35 AM
Replies: 8
Views: 1,799
Posted By AgatheJ
I used the following parameters in...

I used the following parameters in Trimmomatic-0.36:

ILLUMINACLIP:TruSeq2_3-SE.fa:2:30:10 \
SLIDINGWINDOW:100:20 \
HEADCROP:100 \
MINLEN:500 \

I recovered 60,186 reads out of 65,751 and the...
Forum: Genomic Resequencing 02-13-2017, 07:26 AM
Replies: 8
Views: 1,799
Posted By AgatheJ
I guess it is true that I would select for...

I guess it is true that I would select for lower-quality reads in theory, but since I have filtered out low quality reads in the first place (using trimmomatic), maybe that is less of a problem?
...
Forum: Genomic Resequencing 02-13-2017, 06:32 AM
Replies: 8
Views: 1,799
Posted By AgatheJ
Hi Brian, Thanks for your answer! I think...

Hi Brian,

Thanks for your answer!
I think I get duplicates because I had to use multiple PCR steps during library preparation as part of the sequence capture protocol (one round of PCR cycles to...
Forum: Genomic Resequencing 02-13-2017, 04:55 AM
Replies: 8
Views: 1,799
Posted By AgatheJ
Removing duplicate PacBio reads

Hi all,

I think the thread title says it all but below are a bit more details about my problem:

I have used PacBio sequence capture on plant samples and, when looking at my bam files (with...
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