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Search: Posts Made By: GenoMax
Forum: Bioinformatics Yesterday, 05:31 AM
Replies: 87
Views: 13,696
Posted By GenoMax
Are you using the latest version of BBMap? Have...

Are you using the latest version of BBMap? Have you tried to run a test with actual file names instead of shell variables?
Forum: Bioinformatics Yesterday, 04:16 AM
Replies: 87
Views: 13,696
Posted By GenoMax
It looks like out1= and out2= variables are not...

It looks like out1= and out2= variables are not being correctly expanded. BBMap seems to think that your outputs are inputs (in1=./Preproccesing/ERR522065/ERR522065_1_optical.fastq.gz,...
Forum: Bioinformatics 07-19-2018, 11:02 AM
Replies: 2
Views: 136
Posted By GenoMax
Help page ...

Help page (https://software.broadinstitute.org/software/igv/interpreting_insert_size)that describes the meaning of those colors.
Forum: Bioinformatics 07-19-2018, 03:59 AM
Replies: 1
Views: 164
Posted By GenoMax
I am not seeing anything that is an obvious red...

I am not seeing anything that is an obvious red flag. Getting warning in FastQC analysis is common and those need to be taken into consideration using the context of your experiment.

You will...
Forum: Bioinformatics 07-19-2018, 03:57 AM
Replies: 304
Views: 78,447
Posted By GenoMax
@jsena33: You should take a look at UMI tools ...

@jsena33: You should take a look at UMI tools (https://github.com/CGATOxford/UMI-tools)for this type of application.
Forum: Bioinformatics 07-17-2018, 01:59 PM
Replies: 639
Views: 126,838
Posted By GenoMax
Is your bbmap installed correctly? Have you moved...

Is your bbmap installed correctly? Have you moved any files around? I am able to run "bbfakereads.sh" and generate fastq and fasta files without a problem.
Forum: Bioinformatics 07-17-2018, 05:50 AM
Replies: 1
Views: 319
Posted By GenoMax
Export a network share from the CentOS server....

Export a network share from the CentOS server. Mount it on NextSeq 550. You can then choose that share as the destination to write data to. If you don't want to do it that way you could manually copy...
Forum: Bioinformatics 07-12-2018, 08:59 PM
Replies: 304
Views: 78,447
Posted By GenoMax
Have you looked at the in-line help for...

Have you looked at the in-line help for "splitnextera.sh"? The adapters for Mate Pair libraries are in the "adapters.fa" file so you should be able to trim them as usual...
Forum: Bioinformatics 07-11-2018, 01:07 AM
Replies: 2
Views: 374
Posted By GenoMax
You may want to recreate the indexes on WSL and...

You may want to recreate the indexes on WSL and retry. Is the memory availabe comparable on WSL and linux?
Forum: Bioinformatics 07-10-2018, 03:05 AM
Replies: 1
Views: 223
Posted By GenoMax
This is hardly ever the case. Now-a-days...

This is hardly ever the case. Now-a-days technical part of sequencing has become almost perfect. If a lane had some problem (e.g. a bubble during sequencing) your sequencing provider should not...
Forum: Bioinformatics 07-09-2018, 02:26 AM
Replies: 125
Views: 44,813
Posted By GenoMax
I would think so. I don't have first hand...

I would think so. I don't have first hand experience with mate pair reads but I recall that you need to switch one of the reads around.
Forum: Vendor Forum 07-09-2018, 02:23 AM
Replies: 108
Views: 47,450
Posted By GenoMax
Those errors are most likely due to...

Those errors are most likely due to over-clustering or absence of clusters (if at the beginning of the run). Did the run fail? With camera errors it is always good to consult Illumina tech support to...
Forum: Bioinformatics 07-08-2018, 10:19 PM
Replies: 125
Views: 44,813
Posted By GenoMax
Since notes on the page you linked say this: ...

Since notes on the page you linked say this:


You should follow the steps that are denoted to replicate that functionality on the linked page.

In general @Brian has recommended merging reads...
Forum: Bioinformatics 07-08-2018, 11:37 AM
Replies: 125
Views: 44,813
Posted By GenoMax
Can you clarify which program you are referring...

Can you clarify which program you are referring to? I don't think there is a RQCfilter program in BBMap suite.
Forum: Illumina/Solexa 07-05-2018, 10:16 PM
Replies: 2
Views: 458
Posted By GenoMax
You can find the NEBnext adapter sequences in...

You can find the NEBnext adapter sequences in this manual (https://www.neb.com/-/media/catalog/datacards-or-manuals/manuale7335.pdf).
Forum: RNA Sequencing 07-05-2018, 10:14 PM
Replies: 10
Views: 8,960
Posted By GenoMax
Anytime you see low mapping results you should...

Anytime you see low mapping results you should take a sample of reads that don't align and then blast them at NCBI to see if you have

a. Problem with contamination of data with unrelated species...
Forum: RNA Sequencing 07-04-2018, 09:21 PM
Replies: 2
Views: 322
Posted By GenoMax
This question is difficult to answer without...

This question is difficult to answer without access to data. Why did the company used trinity when you have bacterial genomes and don't expect any splicing. Trinity only assembles transcripts and...
Forum: Illumina/Solexa 06-25-2018, 03:19 AM
Replies: 3
Views: 684
Posted By GenoMax
You could run "n+1" cycles and then trim the last...

You could run "n+1" cycles and then trim the last base, if you need that last base. You may want to chat with Illumina support to see if they have an explanation.
Forum: Bioinformatics 06-22-2018, 03:02 AM
Replies: 1
Views: 544
Posted By GenoMax
Take a look at CD-HIT...

Take a look at CD-HIT (http://weizhongli-lab.org/cd-hit/).
Forum: Bioinformatics 06-21-2018, 06:21 AM
Replies: 2
Views: 386
Posted By GenoMax
NCBI requires use of API tokens with eUtils ...

NCBI requires use of API tokens with eUtils (https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/)as May 1st, 2018. It you are running a large amount of queries some of...
Forum: RNA Sequencing 06-20-2018, 01:50 PM
Replies: 2
Views: 662
Posted By GenoMax
Use bbsplit.sh from BBMap to separate human and...

Use bbsplit.sh from BBMap to separate human and mouse reads as shown in this thread (https://www.biostars.org/p/143019/#143040).

SeqAnswers thread page for BBsplit can be found here...
Forum: Illumina/Solexa 06-13-2018, 11:41 AM
Replies: 5
Views: 582
Posted By GenoMax
Good to know. We have a comparatively new machine...

Good to know. We have a comparatively new machine and have not used it a lot. S4 costs add up quickly, though you do get a ton of data.
Forum: Illumina/Solexa 06-13-2018, 05:03 AM
Replies: 5
Views: 582
Posted By GenoMax
We don't have a NextSeq in house so we have not...

We don't have a NextSeq in house so we have not done direct comparisons but as I understand it there are differences in NovaSeq chemistry (for better) compared to NextSeq (hard to find concrete info...
Forum: Bioinformatics 06-13-2018, 04:56 AM
Replies: 304
Views: 78,447
Posted By GenoMax
No hyphens. Just tpe and tbo.

No hyphens. Just tpe and tbo.
Forum: Bioinformatics 06-12-2018, 06:24 PM
Replies: 304
Views: 78,447
Posted By GenoMax
@horvathdp: You can provide NEBnext primers...

@horvathdp: You can provide NEBnext primers (https://www.neb.com/-/media/catalog/datacards-or-manuals/manuale7335.pdf) in a separate file as multi-fasta sequence. Then use that file with bbduk.sh....
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