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Forum: Bioinformatics 03-24-2015, 09:58 AM
Replies: 347
Views: 185,363
Posted By ysnapus
Hi Brian, A couple of quick questions. Since...

Hi Brian,

A couple of quick questions. Since adapters might only have small fragments attached to the ends of the reads, shouldn't we use a smaller mink? The bbduk.sh help lists a default mink=6....
Forum: Bioinformatics 12-01-2014, 04:41 PM
Replies: 347
Views: 185,363
Posted By ysnapus
Perhaps I should generate the SAM file from bbmap...

Perhaps I should generate the SAM file from bbmap and then generate the bhist from just the mapped reads in the SAM? Can a bbmap tool generate the bhist from mapped reads of a SAMfile?

Also, the...
Forum: Bioinformatics 12-01-2014, 03:43 PM
Replies: 347
Views: 185,363
Posted By ysnapus
I am generating the bhist histograms from...

I am generating the bhist histograms from bbmap.sh, so they are after trimming (or before trimming, if I use the untrimmed reads as the input). I generated the figures for both before and after...
Forum: Bioinformatics 12-01-2014, 03:12 PM
Replies: 347
Views: 185,363
Posted By ysnapus
I tried it with more stringent quality trimming...

I tried it with more stringent quality trimming (trimq=20). First of all, in the bbduk.sh stderror output, it says that more than 100% reads were quality trimmed.

Input: 26109034...
Forum: Bioinformatics 12-01-2014, 08:38 AM
Replies: 347
Views: 185,363
Posted By ysnapus
I retried it with quality trimming (qtrim=t),...

I retried it with quality trimming (qtrim=t), removing the last base (ftr=299), and using both nextera and truseq sequences.


in1=../../raw-reads/MiSeq/JBad-Wichita2_140714_R1_001.fastq.gz...
Forum: Bioinformatics 11-17-2014, 07:30 AM
Replies: 347
Views: 185,363
Posted By ysnapus
I ran one of my datasets against both nextera and...

I ran one of my datasets against both nextera and truseq and I still don't get much kmer filtering. Edit: Perhaps I can figure out the adapter sequence from the overlapping read pairs?
java -ea...
Forum: Bioinformatics 11-14-2014, 11:43 AM
Replies: 347
Views: 185,363
Posted By ysnapus
The command line was ~/software/bbmap/bbduk.sh...

The command line was
~/software/bbmap/bbduk.sh in1=../../raw-reads/MiSeq/JBad-Wichita2_${pre}_R1_001.fastq.gz in2=../../raw-reads/MiSeq/JBad-Wichita2_${pre}_R2_001.fastq.gz...
Forum: Bioinformatics 11-14-2014, 08:13 AM
Replies: 347
Views: 185,363
Posted By ysnapus
I am getting something similar with my data. I...

I am getting something similar with my data. I have a couple of questions.

The skewed base content on the left side could be due to the bias in the enzyme mediated fragmentation process(?). Why...
Forum: Bioinformatics 11-12-2014, 11:57 AM
Replies: 347
Views: 185,363
Posted By ysnapus
bbduk2 and some clarifications

Thanks for bringing out a great tool. Noob here so please don't mind some questions, and I hope the answers will be of use to others as well.


I noticed that there is a bbduk.sh and bbduk2.sh...
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