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Search: Posts Made By: GenoMax
Forum: Bioinformatics 09-29-2020, 02:30 AM
Replies: 2
Views: 516
Posted By GenoMax
Cross-posted at biostars:...

Cross-posted at biostars: https://www.biostars.org/p/464101/
Forum: Bioinformatics 09-19-2020, 04:44 AM
Replies: 5
Views: 925
Posted By GenoMax
Create a ticket...

Create a ticket (https://sourceforge.net/projects/bbmap/support) via BBMap's repo so Brian is aware of the problem.
Forum: Bioinformatics 09-17-2020, 08:42 AM
Replies: 5
Views: 925
Posted By GenoMax
I just tried the script and was able to get it to...

I just tried the script and was able to get it to work (did not let it finish). It started making two files. renamed.fa.gz (which has fasta sequences) and badHeaders.txt.

Check to see if you are...
Forum: RNA Sequencing 09-15-2020, 06:16 PM
Replies: 6
Views: 1,344
Posted By GenoMax
You will need to look around to find such data. A...

You will need to look around to find such data. A library run on multiple lanes (which would be technical replicates) may just be concatenated into a single file for analysis and may not be reported...
Forum: General 09-15-2020, 03:02 AM
Replies: 1
Views: 669
Posted By GenoMax
Are you referring to online blast? Please read...

Are you referring to online blast? Please read about the new default blast limits in place: https://www.biostars.org/p/444732/ You would need to change the e-value most likely.
Forum: RNA Sequencing 09-14-2020, 10:37 AM
Replies: 6
Views: 1,344
Posted By GenoMax
No one does technical replicates since they don't...

No one does technical replicates since they don't add any value to the datasets. Are you looking for "biological" replicates?
Forum: Bioinformatics 09-10-2020, 10:37 AM
Replies: 5
Views: 925
Posted By GenoMax
NCBI's FTP site appears to be offline today. So...

NCBI's FTP site appears to be offline today. So that may be one reason why this is not working.
Forum: Bioinformatics 09-04-2020, 09:09 AM
Replies: 2
Views: 1,483
Posted By GenoMax
You can use the "filter" mode for "bbduk.sh" from...

You can use the "filter" mode for "bbduk.sh" from BBMap suite for this. Download the human rDNA repeat (http://www.ncbi.nlm.nih.gov/nuccore/U13369)sequence. Reads that match rDNA can be filtered...
Forum: Illumina/Solexa 09-02-2020, 03:07 AM
Replies: 8
Views: 2,676
Posted By GenoMax
Have you tried to deliberately underload the...

Have you tried to deliberately underload the flowcell? Other option is to try sequencing on MiSeq, undeniable champ of hard to sequence libraries.
Forum: Bioinformatics 09-01-2020, 09:58 AM
Replies: 4
Views: 649
Posted By GenoMax
@kaskere: Were these files compressed using...

@kaskere: Were these files compressed using Windows zip program? You may need to use "-S .zip" option for gunzip.
Forum: Bioinformatics 09-01-2020, 02:51 AM
Replies: 4
Views: 649
Posted By GenoMax
Are you sure the files are gzipped (is spite of...

Are you sure the files are gzipped (is spite of what the extension says)? What does

file one_file.fastq.gz

say?
Forum: Bioinformatics 08-24-2020, 10:54 AM
Replies: 1
Views: 729
Posted By GenoMax
What is not working properly? Indexing genome and...

What is not working properly? Indexing genome and alignment are two independent steps. You completed the indexing of the genome. Now you need to align using `bwa mem`+ this index + your reads =>...
Forum: Sample Prep / Library Generation 08-24-2020, 09:51 AM
Replies: 1
Views: 632
Posted By GenoMax
Cross-posted: https://www.biostars.org/p/457238/

Cross-posted: https://www.biostars.org/p/457238/
Forum: Bioinformatics 08-21-2020, 07:38 AM
Replies: 2
Views: 780
Posted By GenoMax
It is possible that the sequencer may have had...

It is possible that the sequencer may have had trouble with last 6 cycles on read 1 so that part of the data has been trimmed. That can be one explanation. You should be able to use this data...
Forum: Bioinformatics 08-21-2020, 06:08 AM
Replies: 57
Views: 35,435
Posted By GenoMax
Download...

Download (https://sourceforge.net/projects/bbmap/) BBMap suite. "repair.sh" is the program that will sync paired-end data files. It is part of BBtools ahd has a guide available...
Forum: Bioinformatics 08-13-2020, 09:38 AM
Replies: 4
Views: 812
Posted By GenoMax
Rule of thumb is small inserts (and primer...

Rule of thumb is small inserts (and primer dimers) cluster well. So as long as the insert sizes are more or less uniform (and there are no dimers) your results will be as uniform as the pool they can...
Forum: Bioinformatics 08-13-2020, 02:55 AM
Replies: 4
Views: 812
Posted By GenoMax
This is all going to depend on how good your...

This is all going to depend on how good your libraries are and how well balanced a pool you (or your sequencing provider) can make. There should be no bias in data per se just because of how you...
Forum: Illumina/Solexa 08-07-2020, 04:44 AM
Replies: 3
Views: 1,073
Posted By GenoMax
You should be able to do asymmetric runs like...

You should be able to do asymmetric runs like that. But wait for @luc or one of the experimental people to confirm for certain.

As long as there is sequenceable material left there should be no...
Forum: Sample Prep / Library Generation 08-03-2020, 12:37 PM
Replies: 4
Views: 921
Posted By GenoMax
Unique dual indexes are used in library prep. See...

Unique dual indexes are used in library prep. See this. (https://support.illumina.com/bulletins/2018/08/understanding-unique-dual-indexes--udi--and-associated-library-p.html)
Forum: Sample Prep / Library Generation 08-03-2020, 08:57 AM
Replies: 4
Views: 921
Posted By GenoMax
As long as you use unique indexes for all samples...

As long as you use unique indexes for all samples (dual indexes would be best), QC and then balance the libraries in the pool so the contents are more or less uniform, you can mix and sequence these...
Forum: Illumina/Solexa 08-03-2020, 05:39 AM
Replies: 1
Views: 836
Posted By GenoMax
You need to contact Illumina tech support. They...

You need to contact Illumina tech support. They can take a remote look at your machine otherwise ask for some files. Sounds like an hardware issue.
Forum: Bioinformatics 07-27-2020, 05:15 AM
Replies: 2
Views: 709
Posted By GenoMax
Cross-posted and answered at:...

Cross-posted and answered at: https://www.biostars.org/p/451453/
Forum: Sample Prep / Library Generation 07-16-2020, 07:31 AM
Replies: 1
Views: 1,039
Posted By GenoMax
I don't fully understand what you are asking but...

I don't fully understand what you are asking but is this with reference to downstream data analysis (factors to be added in model). Is that correct?
Forum: Illumina/Solexa 07-09-2020, 02:38 AM
Replies: 1
Views: 1,281
Posted By GenoMax
You have a set of indexes there that have a good...

You have a set of indexes there that have a good number of reads. If they don't match indexes you expect then it is a different matter. There is not much you can do about the 20% reads you are losing.
Forum: Bioinformatics 06-20-2020, 07:41 AM
Replies: 14
Views: 9,940
Posted By GenoMax
A long shot. Blast indexes changed to a new...

A long shot. Blast indexes changed to a new version as of Feb 2020. I am not sure where you are running this but if BRIG has not been updated to account for that, it may be causing this problem.
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