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Forum: Bioinformatics 01-24-2020, 02:17 PM
Replies: 2
Views: 162
Posted By GenoMax
How are you running the fastqc program? You re...

How are you running the fastqc program? You re running out of memory.

If you are using the bat file on windows then be sure to edit that and increase the value for memory allocation by changing...
Forum: Bioinformatics 01-24-2020, 04:11 AM
Replies: 3
Views: 346
Posted By GenoMax
How much memory are you assigning to this job?...

How much memory are you assigning to this job? Have these reads been scanned/trimmed before splitting?

Have you also looked at the output of these reports?

scafstats=<file> Write...
Forum: Bioinformatics 01-23-2020, 07:46 AM
Replies: 3
Views: 346
Posted By GenoMax
Have you checked the options about what to do if...

Have you checked the options about what to do if reads are multi-mapping to more than one reference? I am going to hazard a guess that you just have some.
Forum: Bioinformatics 01-21-2020, 10:11 AM
Replies: 1
Views: 106
Posted By GenoMax
Have you checked to make sure that your input...

Have you checked to make sure that your input sequence files are in sync as far as R1/R2 go. You can use `repair.sh` from BBMap suite to bring them in sync if they are not (e.g. if mates are missing...
Forum: Bioinformatics 01-17-2020, 05:23 AM
Replies: 2
Views: 912
Posted By GenoMax
The file extension indicates gzip compression....

The file extension indicates gzip compression. You should be able to use "gunzip" program to uncompress the file. On windows you may want to use a program such as 7-zip to do this conversion.
Forum: Bioinformatics 01-05-2020, 05:01 AM
Replies: 33
Views: 13,143
Posted By GenoMax
@uloeber: @Brian described the method of masking...

@uloeber: @Brian described the method of masking in first post of this thread. It uses "bbmask.sh" which is a component of BBMap suite. Take a look at in-line help for bbmask.sh to get an idea of...
Forum: Bioinformatics 12-31-2019, 03:45 PM
Replies: 2
Views: 1,077
Posted By GenoMax
You can access the normalized counts:...

You can access the normalized counts: https://support.bioconductor.org/p/66067/ Take a look at DESeq2 vignette (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html) for...
Forum: Bioinformatics 12-20-2019, 09:11 AM
Replies: 7
Views: 4,013
Posted By GenoMax
@Luckyboy7: Use deML package to demux your data....

@Luckyboy7: Use deML package to demux your data. More info here (https://github.com/grenaud/deML).
Forum: Bioinformatics 12-13-2019, 03:58 AM
Replies: 2
Views: 723
Posted By GenoMax
Rather than doing the filtering you should...

Rather than doing the filtering you should consider normalizing your data. For this BBMap has another program called bbnorm.sh. You can find a guide here...
Forum: Bioinformatics 12-12-2019, 09:36 AM
Replies: 678
Views: 182,310
Posted By GenoMax
@Robinsleith: I suggest that you post this as a...

@Robinsleith: I suggest that you post this as a ticket (https://sourceforge.net/p/bbmap/tickets/)on BBMap SF page. Brian no longer visits SeqAnswers regularly. He would be the only person who can...
Forum: RNA Sequencing 11-21-2019, 04:31 AM
Replies: 4
Views: 801
Posted By GenoMax
OP says these are from iSeq.

OP says these are from iSeq.
Forum: Bioinformatics 11-21-2019, 04:28 AM
Replies: 4
Views: 609
Posted By GenoMax
@Kapara sometimes reality does not follow what is...

@Kapara sometimes reality does not follow what is written in the paper. Journals don't always enforce these claim submissions so it would be best to email the authors and confirm.
Forum: Bioinformatics 11-20-2019, 04:48 AM
Replies: 4
Views: 609
Posted By GenoMax
People may not always submit the corresponding...

People may not always submit the corresponding assemblies to NCBI. You could email the authors and ask.
Forum: Sample Prep / Library Generation 11-12-2019, 04:59 AM
Replies: 16
Views: 4,750
Posted By GenoMax
Illumina is going to re-introduce ribozero...

Illumina is going to re-introduce ribozero equivalent kits in 2020.
Forum: Bioinformatics 11-08-2019, 08:41 AM
Replies: 1
Views: 520
Posted By GenoMax
Cross-posted and answered on biostars:...

Cross-posted and answered on biostars: https://www.biostars.org/p/407019/
Forum: Bioinformatics 11-08-2019, 06:32 AM
Replies: 2
Views: 613
Posted By GenoMax
You could add a "restrictleft=N" N=certain number...

You could add a "restrictleft=N" N=certain number of bases to look only in that area. Also adding "minlength=N" will exclude small reads like the first example. Also try setting k to something...
Forum: Illumina/Solexa 11-06-2019, 10:22 AM
Replies: 18
Views: 1,254
Posted By GenoMax
That does not jive with read numbers. Are you...

That does not jive with read numbers. Are you referring to 23M total reads (R1+R2) or passing clusters?

That cluster density if not very high to get to 20+M clusters.
Forum: Illumina/Solexa 11-01-2019, 10:16 AM
Replies: 4
Views: 1,166
Posted By GenoMax
I assume you have eliminated a faulty UPS as a...

I assume you have eliminated a faulty UPS as a possible cause? If your sequencer is under a maintenance contract you should contact Illumina tech support ASAP.

Never seen a sequencer just die...
Forum: Illumina/Solexa 11-01-2019, 09:44 AM
Replies: 4
Views: 1,166
Posted By GenoMax
As in the sequencer just died while the power was...

As in the sequencer just died while the power was still on in building? Do you not use UPS's on your sequencers to filter out power anomalies?
Forum: Illumina/Solexa 10-29-2019, 04:14 AM
Replies: 7
Views: 1,327
Posted By GenoMax
You may not have any adapters present if your...

You may not have any adapters present if your inserts were of a good size and there was no read-through.

BBMap suite provides an adapters.fa file in the "resources" directory. You can use it to...
Forum: Illumina/Solexa 10-23-2019, 06:03 AM
Replies: 6
Views: 854
Posted By GenoMax
Smaller inserts do tend to cluster more...

Smaller inserts do tend to cluster more efficiently on flowcells. Can you tell us what the cluster density was? You may need to deliberately underload the run to keep cluster density in check and/or...
Forum: Illumina/Solexa 10-23-2019, 05:52 AM
Replies: 6
Views: 854
Posted By GenoMax
When you say 20 bp span does that mean you have...

When you say 20 bp span does that mean you have just a 20 bp insert?
Forum: Illumina/Solexa 10-23-2019, 05:42 AM
Replies: 7
Views: 1,327
Posted By GenoMax
Do a google search with "QIAseq FX DNA". Second...

Do a google search with "QIAseq FX DNA". Second link in that search should be a PDF file with title "QIAGENŽ QIAseq FX DNA Library Kit Handbook". Check Appendix C in that file for sequences.
...
Forum: Illumina/Solexa 10-23-2019, 05:24 AM
Replies: 2
Views: 1,077
Posted By GenoMax
Yes it is possible to do 384 (and many more if...

Yes it is possible to do 384 (and many more if you do custom designs).



See this page (https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-dna-flex.html).
Forum: RNA Sequencing 10-10-2019, 06:14 AM
Replies: 3
Views: 855
Posted By GenoMax
No need to delete. If someone finds this thread...

No need to delete. If someone finds this thread by search they will know where to get the answer.
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