SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 7 of 7
Search took 0.00 seconds.
Search: Posts Made By: silask
Forum: Bioinformatics 06-06-2018, 04:28 AM
Replies: 3
Views: 911
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 06-03-2018, 11:28 PM
Replies: 3
Views: 911
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 03-21-2018, 11:44 PM
Replies: 126
Views: 45,601
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, 06:27 AM
Replies: 90
Views: 14,492
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, 04:58 AM
Replies: 90
Views: 14,492
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, 02:21 AM
Replies: 90
Views: 14,492
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, 10:52 PM
Replies: 97
Views: 20,260
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...
Showing results 1 to 7 of 7

 


All times are GMT -8. The time now is 02:05 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO