Forum: Bioinformatics
04-16-2020, 02:40 PM
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Replies: 4
Views: 919
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Forum: Bioinformatics
04-16-2020, 09:30 AM
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Replies: 4
Views: 919
I thought Phred+64 was no longer used for...
I thought Phred+64 was no longer used for Illumina scores? I am pretty sure mine is encoded in Phred+33. And I specified qin=33 and qout=33 in the command.
The reason the threshold is 59 is not...
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Forum: Bioinformatics
04-16-2020, 02:28 AM
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Replies: 4
Views: 919
Incorrect bbmap quality trimming
I am using bbmap to trim bases below a certain quality threshold in a FASTQ file. The file looks fine to me in terms of quality scores, but when I run bbmap it trims almost all the bases away and...
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Forum: Illumina/Solexa
03-12-2020, 02:50 PM
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Replies: 7
Views: 2,232
Thanks- that makes sense.
Since I am only...
Thanks- that makes sense.
Since I am only doing a single amplicon, I am wondering if there is a way to do something like this through PCR alone. I would think that if I barcoded each primer, I...
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Forum: Illumina/Solexa
03-09-2020, 02:22 PM
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Replies: 7
Views: 2,232
That is a possibility. I suppose the reason I...
That is a possibility. I suppose the reason I thought 1 in a million would be reasonable is if I set a Phred cutoff of 30 (1 in 1,000), I would think the probability of both paired-end reads having...
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Forum: Illumina/Solexa
03-04-2020, 07:43 PM
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Replies: 7
Views: 2,232
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Forum: Illumina/Solexa
02-19-2020, 05:35 PM
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Replies: 7
Views: 2,232
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