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Forum: Illumina/Solexa 02-10-2021, 12:22 PM
Replies: 2
Views: 471
Posted By GenoMax
It appears to be about 2x faster compared to...

It appears to be about 2x faster compared to bcl2fastq on identical datasets. It is producing different folder structure for result/log files (no more html reports) but plain csv so they should be...
Forum: Bioinformatics 02-04-2021, 05:06 PM
Replies: 7
Views: 3,184
Posted By GenoMax
BBMap suite programs try to auto detect memory...

BBMap suite programs try to auto detect memory available on your system. If they are not able to do that they will fall back to using a safe 2GB using the option mentioned "-Xmx2000m". This is Java...
Forum: Bioinformatics 02-03-2021, 12:35 PM
Replies: 39
Views: 33,047
Posted By GenoMax
Alba: You need to make sure there are no spaces...

Alba: You need to make sure there are no spaces between input options. Try the following.


reformat.sh...
Forum: Bioinformatics 01-31-2021, 02:08 PM
Replies: 1
Views: 494
Posted By GenoMax
If these are prokarotic genomes them Mauve...

If these are prokarotic genomes them Mauve (http://darlinglab.org/mauve/mauve.html) will work. If these are larger eukaryotic genomes them tools like Mugsy (http://mugsy.sourceforge.net/) or MUMMER4...
Forum: Bioinformatics 01-26-2021, 05:53 AM
Replies: 4
Views: 562
Posted By GenoMax
Any reason you are not using an established...

Any reason you are not using an established pipeline like STACKS (https://catchenlab.life.illinois.edu/stacks/).
Forum: Illumina/Solexa 01-25-2021, 10:20 AM
Replies: 3
Views: 616
Posted By GenoMax
Yes they should have demultiplexed after allowing...

Yes they should have demultiplexed after allowing for one error. If they did not then there may be another issue. It would be fair to go back to the facility and ask. If there was a sequencing issue...
Forum: Illumina/Solexa 01-25-2021, 04:27 AM
Replies: 3
Views: 616
Posted By GenoMax
Why is your facility not doing the...

Why is your facility not doing the demultiplexing? This should be very simple for them to do.

It is normal to have a few reads at the beginning of the file to have some N's but are you saying...
Forum: Bioinformatics 11-29-2020, 05:47 PM
Replies: 1
Views: 634
Posted By GenoMax
Cross-posted for reference:...

Cross-posted for reference: https://www.biostars.org/p/476158/
Forum: Illumina/Solexa 11-18-2020, 03:52 AM
Replies: 4
Views: 638
Posted By GenoMax
It is difficult to say what is happening. It may...

It is difficult to say what is happening. It may be fine to use the data. If you have a reference then you could try aligning and see.

There was no known problem with this run correct?
Forum: Illumina/Solexa 11-07-2020, 06:49 AM
Replies: 1
Views: 927
Posted By GenoMax
No big deal. This is normal.

No big deal. This is normal.
Forum: Bioinformatics 09-29-2020, 03:30 AM
Replies: 2
Views: 1,120
Posted By GenoMax
Cross-posted at biostars:...

Cross-posted at biostars: https://www.biostars.org/p/464101/
Forum: Bioinformatics 09-19-2020, 05:44 AM
Replies: 5
Views: 1,352
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, 09:42 AM
Replies: 5
Views: 1,352
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, 07:16 PM
Replies: 6
Views: 1,924
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, 04:02 AM
Replies: 2
Views: 1,850
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, 11:37 AM
Replies: 6
Views: 1,924
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, 11:37 AM
Replies: 5
Views: 1,352
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, 10:09 AM
Replies: 2
Views: 1,855
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, 04:07 AM
Replies: 8
Views: 3,395
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, 10:58 AM
Replies: 4
Views: 942
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, 03:51 AM
Replies: 4
Views: 942
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, 11:54 AM
Replies: 1
Views: 932
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, 10:51 AM
Replies: 1
Views: 1,240
Posted By GenoMax
Cross-posted: https://www.biostars.org/p/457238/

Cross-posted: https://www.biostars.org/p/457238/
Forum: Bioinformatics 08-21-2020, 08:38 AM
Replies: 2
Views: 957
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, 07:08 AM
Replies: 57
Views: 36,590
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...
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