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Forum: Bioinformatics 09-29-2021, 12:40 AM
Replies: 693
Views: 250,689
Posted By silask
bbmap ignores minid

bbmap ignores minid parameter

This is for version 38.93 and 38.92


https://sourceforge.net/projects/bbmap/
Forum: Bioinformatics 06-06-2018, 05:28 AM
Replies: 3
Views: 3,881
Posted By silask
There is still something strange. in the...

There is still something strange.

in the log file of bbwrap I have


* | Paired end | Se
-- | -- | --
Total reads | 2 x 16895000 | 31401969
mapped | 2x 13408609 | 29907540
* | * | *
Forum: Bioinformatics 06-04-2018, 12:28 AM
Replies: 3
Views: 3,881
Posted By silask
Hallo, I assembled metagenomic reads and...

Hallo,

I assembled metagenomic reads and want to know how many reads are mapping to the contigs.

I created a sam file using bbwrap for paired-end libraries with singletons. So the sam files...
Forum: Bioinformatics 03-22-2018, 12:44 AM
Replies: 132
Views: 84,416
Posted By silask
Merge pairs before normalisation?

Hello, I'm building a pipeline for metagenomics.

I follow the bb tools user guide (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/data-preprocessing/) and do:
- normalization with...
Forum: Bioinformatics 12-05-2017, 07:27 AM
Replies: 109
Views: 44,452
Posted By silask
Sorry. For example I have two reads, which are...

Sorry. For example I have two reads, which are 250 and 251 nt long, and identical.
Clumpy doesn't mark them as duplicate even with dupesubs=2. I would say the reads are duplicates, what do you...
Forum: Bioinformatics 12-05-2017, 05:58 AM
Replies: 109
Views: 44,452
Posted By silask
Thank you GenoMax for the quick answer. Ok,...

Thank you GenoMax for the quick answer.

Ok, I see. In the Process guide they don't talk of clumpify. If use clumpify before the trimming I don't have the problem of single-end - paired-end...
Forum: Bioinformatics 12-05-2017, 03:21 AM
Replies: 109
Views: 44,452
Posted By silask
Lightbulb deduplication with clumpify

Hello,

I probably have a problem with PCR duplicates and thought I want to use clumpy to remove duplicates. I did some tests and realised if the reads don't have the same length they are not...
Forum: Bioinformatics 10-22-2017, 11:52 PM
Replies: 104
Views: 48,245
Posted By silask
Hallo, I've a question. The...

Hallo,
I've a question.



The unmerged pairs, are they trimmed or not? Do I have to do a quality trimming again on the unmerged pairs? The same question when using adapter removing during...
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