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Forum: Bioinformatics 01-03-2013, 06:38 PM
Replies: 55
Views: 31,272
Posted By bmtb
Hi again, I just tested the attached copy of...

Hi again,

I just tested the attached copy of the script on 2500 paired seqs and it worked as expected using the following command:

python fastqcombinepairedend.py "@HWI" " " fastq1 fastq2
...
Forum: Bioinformatics 01-03-2013, 06:09 PM
Replies: 55
Views: 31,272
Posted By bmtb
Hi carmeyeii, Sorry it took so long for me...

Hi carmeyeii,

Sorry it took so long for me to reply. If you open the script in a text editor there should be a description in the commented out section at the top of the page. If I recall...
Forum: Bioinformatics 12-17-2012, 03:12 PM
Replies: 29
Views: 9,641
Posted By bmtb
Hi azneto, I guess I should have posted this...

Hi azneto,

I guess I should have posted this earlier, but I actually got your first script to work by increasing the memory allocation. Thanks for the updated script though.

Cheers,
bmtb
Forum: Bioinformatics 12-10-2012, 06:01 PM
Replies: 1
Views: 1,052
Posted By bmtb
Help figuring out variant call format (vcf)

Hi,

I know that there are quite a few threads already on this topic but I can't seem to find any specific to the questions I have. Anyway, I have a vcf file and can't figure out what is going on...
Forum: Bioinformatics 11-29-2012, 03:44 PM
Replies: 29
Views: 9,641
Posted By bmtb
mergeShuffledfastqseqs.pl script issues

I can't get the mergeShuffledFastqSeqs.pl script to work with my data. I have two shuffled paired read files (one is 63GB in size and the other is 35GB). When I submit the job via batch script, it...
Forum: Bioinformatics 10-18-2012, 09:04 AM
Replies: 55
Views: 31,272
Posted By bmtb
Just thought I'd let you know I needed ~227GB of...

Just thought I'd let you know I needed ~227GB of RAM in order to use this script on my data which consisted of two paired-end files 58GB and 29GB in size (after filtering for quality).
Forum: Bioinformatics 10-16-2012, 12:15 PM
Replies: 55
Views: 31,272
Posted By bmtb
Hi again, I just realized my last post with the...

Hi again, I just realized my last post with the correct code didn't keep the indents. so I've attached a file containing the corrected script. To use it remove the .txt extension.

Cheers,
Bryan
Forum: Bioinformatics 10-16-2012, 12:07 PM
Replies: 55
Views: 31,272
Posted By bmtb
Thanks Jackie! I tried the revised script but it...

Thanks Jackie! I tried the revised script but it still didn't work correctly. Only after I went through the script re-setting all the indents and after correcting some lines did I manage to get it...
Forum: Bioinformatics 10-14-2012, 06:23 PM
Replies: 55
Views: 31,272
Posted By bmtb
Hello again, so I made several attempts to use...

Hello again, so I made several attempts to use the PECombiner.sh/fastqcombinepairedreads.py script to work on my paired reads but Jackie previously noted the script is faulty.
Forum: Bioinformatics 10-14-2012, 04:03 PM
Replies: 55
Views: 31,272
Posted By bmtb
Thanks Jackie! I downloaded the scripts available...

Thanks Jackie! I downloaded the scripts available from the link you posted and checked the PEcombine.sh script, and it appears to be exactly what I need. I'll post again to let those interested know...
Forum: Bioinformatics 10-12-2012, 02:52 PM
Replies: 55
Views: 31,272
Posted By bmtb
matching up paired-end reads after fastx-toolkit filtering

Hi,

I just learned that most genome assemblers rely on the order of sequences within paired read files to maintain read pairings. Unfortunately, I have already gone and processed each of my...
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