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Forum: Illumina/Solexa 03-05-2021, 07:41 PM
Replies: 7
Views: 150
Posted By GenoMax
That would be fine. Edit: SNPSarus makes a...

That would be fine.

Edit: SNPSarus makes a good point below. If the gene density of your organism is similar then an equivalent reduction would be fine. Otherwise scale accordingly.
Forum: Illumina/Solexa 03-05-2021, 05:13 PM
Replies: 7
Views: 150
Posted By GenoMax
Generally for human samples (3 gb genome) one...

Generally for human samples (3 gb genome) one would want to target around 25-30 Million reads per sample. So use that as an approximation to calculate the number of reads you would need per sample.
...
Forum: Illumina/Solexa 03-04-2021, 07:02 AM
Replies: 2
Views: 158
Posted By GenoMax
Since the sequencer is a precision instrument you...

Since the sequencer is a precision instrument you will take usual precautions if you had to move it. In any case it will have to be re-certified by the engineer after it is moved back in place.
...
Forum: Illumina/Solexa 03-01-2021, 05:52 AM
Replies: 1
Views: 170
Posted By GenoMax
You should be able to run MiSeq nano FC (~1 M...

You should be able to run MiSeq nano FC (~1 M clusters) to check the balance of libraries and most of all to verify that libraries have worked. We routinely do that for pools destined for NovaSeq.
Forum: Illumina/Solexa 02-10-2021, 12:22 PM
Replies: 2
Views: 539
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: 3,276
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: 33,333
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: 567
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: 646
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: 674
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: 674
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: 682
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: 701
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: 987
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: 1,141
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: 1,383
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: 1,383
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: 1,977
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: 1,909
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: 1,977
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: 1,383
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: 1,884
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: 3,476
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: 971
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: 971
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?
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