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Search: Posts Made By: kokyriakidis
Forum: Bioinformatics 07-27-2018, 10:26 PM
Replies: 46
Views: 20,954
Posted By kokyriakidis
Hello! I have RNA-Seq data and I am processing...

Hello! I have RNA-Seq data and I am processing them with BBtools for adapter trimming, quality trimming, contaminant filtering, error correction. I want to use these data as support in denovo genome...
Forum: Bioinformatics 07-23-2018, 11:02 AM
Replies: 90
Views: 15,033
Posted By kokyriakidis
I am having trouble using clumpify with the...

I am having trouble using clumpify with the parameters optical + dedupe, to remove optical duplicates. e.x. clumpify.sh in=temp.fq.gz out=clumped.fq.gz dedupe optical. Clumpify without these...
Forum: Bioinformatics 07-23-2018, 08:19 AM
Replies: 90
Views: 15,033
Posted By kokyriakidis
I use the latest version of BBtools. I can't get...

I use the latest version of BBtools. I can't get it work
Forum: Bioinformatics 07-21-2018, 04:21 AM
Replies: 90
Views: 15,033
Posted By kokyriakidis
Yes! all files are in the same folder! Actually...

Yes! all files are in the same folder! Actually neither clumpify dedupe optical, nor filterbytile work. So I have to remove them in order to complete my pipeline...
Forum: Bioinformatics 07-21-2018, 12:46 AM
Replies: 90
Views: 15,033
Posted By kokyriakidis
After clumpify command to remove duplicates using...

After clumpify command to remove duplicates using in1 in2 and out1 out2, it seems like it produces only 1 out, messing with the pipeline stream! Why does it happen?

./bbmap/clumpify.sh...
Forum: Bioinformatics 07-12-2018, 09:24 PM
Replies: 304
Views: 81,652
Posted By kokyriakidis
Different Libraries

In SplitNextera guide it states that it it different from LMP. Nextera mate pair is not the same as Mate pair library v2 and also, Mate pair library v2 does not have these LMP adapters you mentioned!...
Forum: Bioinformatics 07-12-2018, 04:24 AM
Replies: 304
Views: 81,652
Posted By kokyriakidis
Genomax, do we have to trim Mate pair reads...

Genomax, do we have to trim Mate pair reads differently? I ask because they have the internal adapter. I am not asking about the Nextera mate pair. I ask for the reads made by MatePairSamplePrep v2....
Forum: Bioinformatics 07-08-2018, 10:25 PM
Replies: 126
Views: 46,666
Posted By kokyriakidis
In long pair mate reads I just do the...

In long pair mate reads I just do the splitNextera extra step? Otherwise the pipeline remains the same?
Forum: Bioinformatics 07-08-2018, 12:11 PM
Replies: 126
Views: 46,666
Posted By kokyriakidis
Source:...

Source: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/data-preprocessing/

"These steps replicate the QA protocol implemented at JGI for Illumina reads. There is a program...
Forum: Bioinformatics 07-08-2018, 12:02 PM
Replies: 304
Views: 81,652
Posted By kokyriakidis
trimming Long and Short

Hi, do I need to follow a different approach in trimming and filtering Short vs long mate pair reads (Nextera)? And if yes could someone elaborate the pipeline?
Forum: Bioinformatics 07-08-2018, 10:28 AM
Replies: 126
Views: 46,666
Posted By kokyriakidis
RQCFilter Norm and EC

Hi Brian,

I am trying to trim and filter my data with RQCFilter but I cannot find an option for normalisation and error correction. Are there any parameters in this package? Also there is a...
Forum: Bioinformatics 07-07-2018, 11:46 AM
Replies: 97
Views: 21,184
Posted By kokyriakidis
RQCFilter Norm and ECC

Hello!

Does RQCFilter has a parameter to normalise and error correct? Or I should do it afterwards?
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