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Search: Posts Made By: mcrawford
Forum: Bioinformatics 10-31-2016, 09:11 AM
Replies: 2
Views: 2,030
Posted By mcrawford
Thanks very much for the reply, this works :) ...

Thanks very much for the reply, this works :)

In case this helps anyone else, I am on Windows, so I run BBDuk like this:
java -ea -Xmx200m -cp C:\bbmap\current\ jgi.BBDuk2 in1=Sample_R1.fastq...
Forum: Bioinformatics 10-31-2016, 07:52 AM
Replies: 2
Views: 2,030
Posted By mcrawford
FastQ: trimming paired reads down to a set length

Hello,

I have some 2x300bp sequencing data and I want to treat it as if it were a 2x100bp run.

So, I have some paired-read FastQs with reads of all different lengths, up to 300bp. I want to...
Forum: Bioinformatics 09-23-2015, 01:06 AM
Replies: 2
Views: 860
Posted By mcrawford
Thanks so much GenoMax, this worked perfectly and...

Thanks so much GenoMax, this worked perfectly and produced exactly what I wanted! You're the best :)
Forum: Bioinformatics 09-22-2015, 07:17 AM
Replies: 2
Views: 860
Posted By mcrawford
Need my reference sequence to be in a specific format

I need my reference genome (S. cerevisiae strain S288c) to be in a specific format for some analysis but can't find anything matching what I need online.

i.e. the data I have is in this format:...
Forum: Bioinformatics 06-12-2015, 05:05 AM
Replies: 10
Views: 1,758
Posted By mcrawford
OK, I added the full path to each filename and it...

OK, I added the full path to each filename and it works now! Thanks for all the help in this thread :)
Forum: Bioinformatics 06-12-2015, 04:55 AM
Replies: 10
Views: 1,758
Posted By mcrawford
Thanks so much! Adding '-cp' works. However... it...

Thanks so much! Adding '-cp' works. However... it now can't find my .sam file. Which folder is it looking in? I tried putting the file in the 'bbmap', 'current' and 'jgi' folders. Or do I need the...
Forum: Bioinformatics 06-12-2015, 03:36 AM
Replies: 10
Views: 1,758
Posted By mcrawford
Yes, there is a space. I didn't move any files...

Yes, there is a space. I didn't move any files either, but I might try re-downloading bbmap just in case.
Forum: Bioinformatics 06-12-2015, 02:48 AM
Replies: 10
Views: 1,758
Posted By mcrawford
Yes, it is under C:\ (I deliberately put it there...

Yes, it is under C:\ (I deliberately put it there to make the path nice and short :))
Forum: Bioinformatics 06-12-2015, 02:05 AM
Replies: 10
Views: 1,758
Posted By mcrawford
Thank you very much for your reply! I am now...

Thank you very much for your reply!

I am now trying to run bbmap reformat on Windows via the command line by entering:

java -ea -Xmx200m C:\bbmap\current\ jgi.ReformatReads in=reads.sam...
Forum: Bioinformatics 06-11-2015, 05:00 AM
Replies: 10
Views: 1,758
Posted By mcrawford
How to isolate and examine discordant pairs?

Hello,
I am examining yeast that have undergone meiotic recombination, using paired-end sequencing on the Illumina MiSeq and aligned with bowtie2.
I want to look in my sequencing data for ectopic...
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