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Search: Posts Made By: GenoMax
Forum: Bioinformatics Today, 10:27 AM
Replies: 198
Views: 40,260
Posted By GenoMax
BBTools currently has no count utilities. They...

BBTools currently has no count utilities. They may be on the wish list since many have asked Brian. For now, your best bet is to use featureCounts (http://bioinf.wehi.edu.au/featureCounts/).
Forum: Illumina/Solexa Today, 04:25 AM
Replies: 2
Views: 71
Posted By GenoMax
Here is Illumina's official take on the amount of...

Here is Illumina's official take on the amount of reagents available (https://support.illumina.com/bulletins/2016/10/how-many-cycles-of-sbs-chemistry-are-in-my-kit.html) in all kits.
Forum: Bioinformatics 12-08-2017, 11:49 AM
Replies: 2
Views: 205
Posted By GenoMax
Do you have access to a linux machine? If so save...

Do you have access to a linux machine? If so save the two files in plain text format from excel (tab delimited for the annotation is fine). Then you can do something like

grep -f file_with_ID...
Forum: General 12-08-2017, 08:14 AM
Replies: 2
Views: 151
Posted By GenoMax
No "make" is needed for BBMap suite. Only...

No "make" is needed for BBMap suite. Only requirement is Java. Download BBMap code archive, uncompress and then start using.
Forum: Illumina/Solexa 12-08-2017, 05:23 AM
Replies: 9
Views: 386
Posted By GenoMax
It is interesting if they actually said that....

It is interesting if they actually said that. Perhaps they did not want to spook you :)



That is to be expected. When a run is overclustered the clusters are very close to begin with. Over the...
Forum: Bioinformatics 12-07-2017, 11:25 AM
Replies: 2
Views: 215
Posted By GenoMax
No script should be needed. Use BioMart to do...

No script should be needed. Use BioMart to do this yourself.

Go to Ensembl (http://www.ensembl.org/index.html). Click on BioMart link at the top. A new page should open. Going to show an example...
Forum: Illumina/Solexa 12-07-2017, 09:02 AM
Replies: 9
Views: 386
Posted By GenoMax
You are way over spec for the cluster density. I...

You are way over spec for the cluster density. I am surprised you were able to get any data at all. I would not trust the data you have if it is to be used for any type of de novo work. You should...
Forum: Ion Torrent 12-05-2017, 10:02 AM
Replies: 8
Views: 424
Posted By GenoMax
Are you referring to targeted amplicon sequencing...

Are you referring to targeted amplicon sequencing for RNAseq?
Forum: Bioinformatics 12-05-2017, 07:56 AM
Replies: 83
Views: 10,901
Posted By GenoMax
Interesting point. I have always worked with data...

Interesting point. I have always worked with data that was of uniform length. Based on what you have discovered clumpify does seem to have an underlying need/assumption that the reads are all equal...
Forum: Bioinformatics 12-05-2017, 06:11 AM
Replies: 83
Views: 10,901
Posted By GenoMax
I am not sure exactly what you are referring to....

I am not sure exactly what you are referring to. Clumpify by default will allow two substations (errors if you will). If you want to do strict matching then use dupesubs=0. Can you include the...
Forum: Bioinformatics 12-05-2017, 04:18 AM
Replies: 2
Views: 274
Posted By GenoMax
Are you able to list the file by doing an ls with...

Are you able to list the file by doing an ls with full path?
Forum: Bioinformatics 12-05-2017, 04:14 AM
Replies: 83
Views: 10,901
Posted By GenoMax
Here is my take (could be wrong). That processing...

Here is my take (could be wrong). That processing guide may have been written before clumpify existed. You should use clumpify on raw data (before anything is done to it). That is the best way to...
Forum: Ion Torrent 12-04-2017, 08:57 AM
Replies: 8
Views: 424
Posted By GenoMax
It is not that it can't be used. It is more that...

It is not that it can't be used. It is more that you should not be using TopHat pipeline for any new data. TopHat is in maintenance mode and even its developers recommend that you use HISAT2, their...
Forum: Ion Torrent 12-04-2017, 08:20 AM
Replies: 8
Views: 424
Posted By GenoMax
Tools for Illumina should be fine to use for Ion...

Tools for Illumina should be fine to use for Ion Torrent data as well since you still have fastq data. There may be biases/other issues with Ion torrent that you would need to keep in mind (e.g....
Forum: Bioinformatics 12-04-2017, 07:01 AM
Replies: 198
Views: 40,260
Posted By GenoMax
Have you looked through the logs and such to see...

Have you looked through the logs and such to see if there is any indication of any issues? There is always the possibility that @Brian may not have checked extreme usage case like this for...
Forum: Bioinformatics 12-04-2017, 06:20 AM
Replies: 198
Views: 40,260
Posted By GenoMax
@Brian will likely have to weigh in on this...

@Brian will likely have to weigh in on this (especially "positions stated in read header with the actual read sequence, for most of the reads they were too different ") but be aware that he has been...
Forum: Bioinformatics 12-04-2017, 04:32 AM
Replies: 198
Views: 40,260
Posted By GenoMax
How similar are those 1000 genomes? What...

How similar are those 1000 genomes? What parameters are you using related to multi-mapping with BBMap? As the number of similar genomes increases the numbers of reads that multi-map will go up as...
Forum: Bioinformatics 11-29-2017, 10:56 AM
Replies: 1
Views: 354
Posted By GenoMax
There should be no difference in the sequence...

There should be no difference in the sequence since it is the same genome build. As you discovered, UCSC uses a "chr" prefix for chromosomes whereas Ensembl uses plain numbers (e.g. 1). Some finer...
Forum: Illumina/Solexa 11-29-2017, 05:59 AM
Replies: 3
Views: 377
Posted By GenoMax
Bead washing the pool may also help remove excess...

Bead washing the pool may also help remove excess primers etc. There are other threads on here that go into specifics of how you would use that or someone else with experimental expertise will post...
Forum: Bioinformatics 11-29-2017, 05:56 AM
Replies: 2
Views: 358
Posted By GenoMax
@John: I have not seen this error before either....

@John: I have not seen this error before either. Your original commands should have been fine.

I suggest that you email blast helpdesk with this error. It would be great if you can post their...
Forum: Illumina/Solexa 11-29-2017, 04:27 AM
Replies: 3
Views: 377
Posted By GenoMax
As long as you are using dual indexing chances of...

As long as you are using dual indexing chances of mis-assignment of indexes is significantly reduced. See this white paper from Illumina ...
Forum: Pacific Biosciences 11-27-2017, 06:11 PM
Replies: 5
Views: 669
Posted By GenoMax
Post some of the stats from your HGAP.4 run. Dr....

Post some of the stats from your HGAP.4 run. Dr. Hall will likely need those to comment further.
Forum: Bioinformatics 11-27-2017, 06:41 AM
Replies: 2
Views: 399
Posted By GenoMax
This question is cross-posted and has been...

This question is cross-posted and has been answered: https://www.biostars.org/p/282328/#286154
Forum: RNA Sequencing 11-27-2017, 05:22 AM
Replies: 2
Views: 336
Posted By GenoMax
That will work. How did you handle multi-mappers...

That will work. How did you handle multi-mappers during alignment? That can skew some of your counts.
Forum: Illumina/Solexa 11-26-2017, 05:03 AM
Replies: 12
Views: 952
Posted By GenoMax
True. There is a reason not to be easily able to...

True. There is a reason not to be easily able to mess with a sequencer certified for clinical sequencing.

That said, Nextseq 550Dx (newly certified NextSeq for Clinical applications) supposedly...
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