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Search: Posts Made By: maxz411
Forum: Bioinformatics 04-16-2020, 01:40 PM
Replies: 4
Views: 756
Posted By maxz411
Ah I figured out what was happening. Your comment...

Ah I figured out what was happening. Your comment about the high Phred scores got me thinking on the right track. After looking at the documentation further it seems that bbmap has a flag to cap base...
Forum: Bioinformatics 04-16-2020, 08:30 AM
Replies: 4
Views: 756
Posted By maxz411
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...
Forum: Bioinformatics 04-16-2020, 01:28 AM
Replies: 4
Views: 756
Posted By maxz411
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...
Forum: Illumina/Solexa 03-12-2020, 01:50 PM
Replies: 7
Views: 2,106
Posted By maxz411
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...
Forum: Illumina/Solexa 03-09-2020, 01:22 PM
Replies: 7
Views: 2,106
Posted By maxz411
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...
Forum: Illumina/Solexa 03-04-2020, 06:43 PM
Replies: 7
Views: 2,106
Posted By maxz411
Thank you! And sorry for the delayed response- I...

Thank you! And sorry for the delayed response- I wanted to read through your PELE-seq paper as well as the one on ENU-induced mutagenesis, since that is what I am doing (in cells though, not in...
Forum: Illumina/Solexa 02-19-2020, 04:35 PM
Replies: 7
Views: 2,106
Posted By maxz411
Overlapping paired-end reads for rare mutation detection

I am new to next-generation sequencing but am interested in using it to detect rare random mutations induced in a population of cells by exposure to a mutagen. I am interested in getting 50,000 reads...
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