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Forum: Metagenomics 02-05-2016, 07:28 AM
Replies: 3
Views: 2,288
Posted By salamay
I never did end up solving this with MEGAN, so...

I never did end up solving this with MEGAN, so thanks for posting your solution! I ended up analyzing each member of the paired reads separately and then I just wrote my own script to combine the...
Forum: Bioinformatics 01-05-2016, 11:44 AM
Replies: 327
Views: 98,773
Posted By salamay
Hi Brian, Would you mind explaining the the...

Hi Brian,

Would you mind explaining the the sliding window option for quality trimming (qtrim) in bbduk? How big is the window and is this similar to trimmomatic's sliding window approach? I...
Forum: Bioinformatics 12-07-2015, 11:40 AM
Replies: 218
Views: 125,621
Posted By salamay
Hi Alex, Your software is really great! I...

Hi Alex,

Your software is really great! I had a quick question about the --quantMode GeneCounts function. I seem to be getting mostly noFeature hits. This is what is in my ReadsPerGene.out.tab...
Forum: Metagenomics 11-11-2015, 12:59 PM
Replies: 3
Views: 2,288
Posted By salamay
Exclamation Paired-read analysis in MEGAN

I am attempting to utilize blastn output from paired end files for MEGAN analysis. However, selecting the paired-read checkbox in the "import from blast" window does not seem to work. I have tried...
Forum: Bioinformatics 04-01-2015, 07:18 AM
Replies: 2
Views: 1,553
Posted By salamay
Thank you very much yzzhang, that worked...

Thank you very much yzzhang, that worked perfectly. I was incorrectly assuming that a gi to taxon file was provided by default. Thanks again.
Forum: Bioinformatics 03-31-2015, 08:41 AM
Replies: 2
Views: 1,553
Posted By salamay
sam2rma Tool in MEGAN

Has anyone been able to use the sam2rma standalone tool provided with MEGAN? I can't seem to get it to perform taxonomic classification, although I can get functional classification through KEGG,...
Forum: Bioinformatics 12-09-2014, 09:05 AM
Replies: 0
Views: 1,033
Posted By salamay
Unhappy GNU Parallel Losing Records

I am using GNU parallel to speed up BLAST and I am using this command:

cat test.fna | parallel --gnu --block 100k --recstart '>' --pipe blastn -db database -query - > test.fna.blastn

I am...
Forum: Bioinformatics 12-03-2014, 07:03 AM
Replies: 6
Views: 1,249
Posted By salamay
Increasing the threads definitely helps. I guess...

Increasing the threads definitely helps. I guess I'll fiddle around with that. Thanks GenoMax!
Forum: Bioinformatics 12-03-2014, 06:37 AM
Replies: 6
Views: 1,249
Posted By salamay
The machine I run the searches on is a 48 core...

The machine I run the searches on is a 48 core 2.7ghz with 264 Gb RAM, but not sure how much of that is allocated for the search (nor do I know how to specify allocation). I run the search with...
Forum: Bioinformatics 12-03-2014, 06:28 AM
Replies: 6
Views: 1,249
Posted By salamay
BLASTX Issues

I am attempting to run blastx from the command line, and it seems to be very slow (~5-6 minutes for 10 100bp sequences). I compared this to blastx on the NCBI website, which took only 30 seconds....
Forum: Bioinformatics 07-09-2014, 11:48 AM
Replies: 128
Views: 52,912
Posted By salamay
Hi Brian, Could you try benchmarking against...

Hi Brian,

Could you try benchmarking against SeqPreP (https://github.com/jstjohn/SeqPrep)?
Forum: Bioinformatics 07-08-2014, 07:30 AM
Replies: 3
Views: 1,627
Posted By salamay
Well I don't think it is optimal to provide only...

Well I don't think it is optimal to provide only one hit when using a lowest common ancestor algorithm which MEGAN uses so I would probably not use -max_target_seqs 1 and just let it get as many...
Forum: Bioinformatics 07-04-2014, 06:32 AM
Replies: 3
Views: 1,627
Posted By salamay
Are you manually setting the number of hits...

Are you manually setting the number of hits returned to 1 or do all your sequences that have hits actually only return 1 hit?
In any case, I believe going into options->change LCA paramters, and...
Forum: Bioinformatics 07-03-2014, 10:04 AM
Replies: 327
Views: 98,773
Posted By salamay
That is extremely informative Brian. Thank you...

That is extremely informative Brian. Thank you very much, I am very pleased with the bb suite of programs.
Forum: Bioinformatics 07-03-2014, 09:48 AM
Replies: 327
Views: 98,773
Posted By salamay
What would bbduk do if for instance the right and...

What would bbduk do if for instance the right and left ends were high quality but a region in the middle of the read was low quality? For instance:

40, 40, 40, 40, 2, 2, 2, 40, 40, 40

Your...
Forum: Bioinformatics 07-03-2014, 07:53 AM
Replies: 327
Views: 98,773
Posted By salamay
Hi Brian, Can you elaborate on what you mean...

Hi Brian,

Can you elaborate on what you mean by the quality trimming is done using the Phred algorithm and how this is more accurate than naive trimming?

Thank you
Forum: Bioinformatics 06-04-2014, 12:26 PM
Replies: 8
Views: 2,513
Posted By salamay
I believe so but I am not sure and have asked...

I believe so but I am not sure and have asked those responsible for the generation of the data. Would using a nextera kit explain what is seen?
Forum: Bioinformatics 06-04-2014, 10:16 AM
Replies: 8
Views: 2,513
Posted By salamay
Thanks lac302, from what I have done so far I...

Thanks lac302, from what I have done so far I have trimmed the sequences up to bp 16 and worked from there as you seem to have done but I can't figure out the cause for it or whether it is a bit...
Forum: Bioinformatics 06-04-2014, 06:49 AM
Replies: 8
Views: 2,513
Posted By salamay
Thanks tonybrooks, yes it was on a hiseq. I had...

Thanks tonybrooks, yes it was on a hiseq. I had not heard about this issue before thanks for bringing it to my attention.
Forum: Bioinformatics 06-04-2014, 06:04 AM
Replies: 8
Views: 2,513
Posted By salamay
FASTQC trends

I have some metagenomic data obtained from whole genome shotgun sequencing using illumina-hiseq. The reads are 100bp paired end and when I examine the reads in fastqc, I see a couple of things....
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