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Search: Posts Made By: darthsequencer
Forum: Bioinformatics 08-21-2019, 03:43 PM
Replies: 240
Views: 83,965
Posted By darthsequencer
Is there a command to output the kmers of each...

Is there a command to output the kmers of each sequence in a multifasta file?
Forum: Bioinformatics 06-01-2018, 12:14 PM
Replies: 240
Views: 83,965
Posted By darthsequencer
Is there a multi-sample pileup? I have a bunch of...

Is there a multi-sample pileup? I have a bunch of samples mapped to the same reference. It would be awesome to have that as a table with the coverage for each sample per reference sequence.
Forum: Bioinformatics 04-27-2018, 01:41 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Hi Brian, I'm using trimrname=t from...

Hi Brian,
I'm using trimrname=t from reformat.sh on a sam file. It looks like it trims the ref names correctly on the alignment lines, but not in header lines (the ones that start with @).
Forum: Bioinformatics 04-17-2018, 11:36 AM
Replies: 674
Views: 170,650
Posted By darthsequencer
Hi Brian - Is there a bbtool that will keep only...

Hi Brian - Is there a bbtool that will keep only mapped reads and if the mate doesn't map output the unmapped also from sam/bam files?

Thanks
Forum: Bioinformatics 03-15-2018, 09:03 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Yeah - I have but from what I can tell it maxes...

Yeah - I have but from what I can tell it maxes out at 6 reports unless maxsites is increased. I am wondering if there is a setting that avoids maxsites and reports everything above some score.
Forum: Bioinformatics 03-15-2018, 12:38 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Hi Brian - What are the right flags to set if I...

Hi Brian - What are the right flags to set if I want all of the top scoring mappings for paired end reads?

Thanks
Forum: Bioinformatics 09-07-2017, 10:34 AM
Replies: 674
Views: 170,650
Posted By darthsequencer
Hi - So if I set secondarysitescoreratio to 1.0...

Hi - So if I set secondarysitescoreratio to 1.0 do I need to set secondary = T if ambiguous=all and increase the maxsites setting?

I guess what I'm really asking is what do I need to set to ensure...
Forum: Bioinformatics 08-09-2017, 02:24 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Thanks that's helpful. On the note of loading...

Thanks that's helpful. On the note of loading references - is there a way to use wildcards with the input and output of bbwrap?
Forum: Bioinformatics 08-09-2017, 02:04 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
They range between 50bp single end to 2 x 250bp

They range between 50bp single end to 2 x 250bp
Forum: Bioinformatics 08-09-2017, 10:29 AM
Replies: 674
Views: 170,650
Posted By darthsequencer
bbmap fast macro?

Hi Brian,
I have a lot of reference sequences I'm mapping to (~11 million) and want to eek out as much as speed as possible.

I'm mostly looking for close matches - ex. I set minid to 0.97. Will...
Forum: Bioinformatics 08-09-2017, 10:23 AM
Replies: 674
Views: 170,650
Posted By darthsequencer
Thanks- that helps a lot!

Thanks- that helps a lot!
Forum: Bioinformatics 07-31-2017, 07:51 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Hi - I love that bbmap and its tools can directly...

Hi - I love that bbmap and its tools can directly make bam files. I noticed that it's using samtools with 8 threads. Is there a way to increase the number of threads?

Thanks
Forum: Bioinformatics 05-23-2017, 03:46 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Hi I gave that a shot and dedupe throws a bunch...

Hi I gave that a shot and dedupe throws a bunch of errors and produces about double the clusters than dedupe does without clustering.

Here's a copy of log:...
Forum: Bioinformatics 05-23-2017, 10:48 AM
Replies: 674
Views: 170,650
Posted By darthsequencer
Hi Brian - I think "renamecluster=t" in dedupe.sh...

Hi Brian - I think "renamecluster=t" in dedupe.sh will do what I want with regards to tracking which contigs are greater than "minidentity".

I run dedupe.sh like this: dedupe.sh in=file.fa...
Forum: Bioinformatics 05-03-2017, 10:14 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Does this work with paired end reads? I get...

Does this work with paired end reads?

I get this error: Read of length 36 outside of range 50--1. Paired input is incompatible with 'breaklength'
Forum: Bioinformatics 05-02-2017, 07:14 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Great! Yeah I'd like to know the duplicate...

Great! Yeah I'd like to know the duplicate membership for containments too.
Forum: Bioinformatics 05-02-2017, 05:13 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Well my real use it to group sequences that >99%...

Well my real use it to group sequences that >99% similar. Whereas clumpify find exact matches? Although I suppose that clumpify could be run in error correct mode with "midid" and it should be the...
Forum: Bioinformatics 05-02-2017, 12:30 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Did anything like this get added to BBMap? Would...

Did anything like this get added to BBMap? Would be really helpful for me too!
Forum: Bioinformatics 05-02-2017, 12:25 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Oh yeah - duh

Oh yeah - duh
Forum: Bioinformatics 05-02-2017, 12:00 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Thanks for the tip - save me some space so I...

Thanks for the tip - save me some space so I don't have to make additional files. I deal with a lot of libraries with different read lengths.

Is there a way to make BBMap require the smallest...
Forum: Bioinformatics 05-02-2017, 11:31 AM
Replies: 674
Views: 170,650
Posted By darthsequencer
Hi Brian, Is there a way to set a minimum input...

Hi Brian,
Is there a way to set a minimum input fragment length when mapping with BBMap?
Forum: Bioinformatics 11-08-2016, 02:22 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Great - Thanks a bunch!

Great - Thanks a bunch!
Forum: Bioinformatics 11-08-2016, 11:03 AM
Replies: 674
Views: 170,650
Posted By darthsequencer
That would be awesome Brian! Most of the tools...

That would be awesome Brian! Most of the tools out there are bit wonky, slow, or have fallen to the wayside.

More of a nuts and bolts question but how do you handle fragmented reference genomes...
Forum: Bioinformatics 11-07-2016, 06:54 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Hi Brian, Is there a way to set a desired...

Hi Brian,
Is there a way to set a desired coverage for randomreads.sh rather than the total number of reads?

On that note - I'm trying to simulate a metagenome with bbmap tools. Knowing BBMap...
Forum: Bioinformatics 08-14-2016, 12:14 PM
Replies: 674
Views: 170,650
Posted By darthsequencer
Hi I have a couple questions on the terminology...

Hi I have a couple questions on the terminology used for retaining ambiguous sites using bbmap.

If "ambiguous=best" this means that if there are a bunch of reads all the with the sam score only...
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