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Search: Posts Made By: GenoMax
Forum: Bioinformatics 10-13-2021, 11:47 AM
Replies: 347
Views: 185,363
Posted By GenoMax
DP: You should use `bbsplit.sh` to do...

DP: You should use `bbsplit.sh` to do read-binning to remove host data contamination. There is a thread here that describes how to use that tool.

Use bbduk for just adapter removal. Using it in...
Forum: Bioinformatics 09-28-2021, 03:13 AM
Replies: 347
Views: 185,363
Posted By GenoMax
@lituan you will need to use k=2 or less with...

@lituan you will need to use k=2 or less with such a short pattern (CCGG). Even then it may not work well.

This may be a case where you would want to use a different package called Seqkit...
Forum: Bioinformatics 09-09-2019, 07:57 PM
Replies: 347
Views: 185,363
Posted By GenoMax
You can simply capture the STDERR output (where...

You can simply capture the STDERR output (where this is bring written) to a file (https://askubuntu.com/questions/625224/how-to-redirect-stderr-to-a-file).
Forum: Bioinformatics 02-26-2019, 04:42 AM
Replies: 347
Views: 185,363
Posted By GenoMax
@aushev: Unfortunately Brian no longer has time...

@aushev: Unfortunately Brian no longer has time to participate on this forum. He would really be the only person who can authoritatively answer your questions. You could try to create a ticket on SF...
Forum: Bioinformatics 02-25-2019, 04:11 PM
Replies: 347
Views: 185,363
Posted By GenoMax
Any reads that align to the ribosomal repeat will...

Any reads that align to the ribosomal repeat will be identified and separated in a file. Isn't that what you are looking to do?
Forum: Bioinformatics 02-25-2019, 11:12 AM
Replies: 347
Views: 185,363
Posted By GenoMax
@aushev: That k-mers file is likely for non-human...

@aushev: That k-mers file is likely for non-human genomes since it was made from SILVA database.

You could use U13369 fasta sequence and then bin the reads that map to it using bbsplit.sh.
Forum: Bioinformatics 02-07-2019, 03:46 AM
Replies: 347
Views: 185,363
Posted By GenoMax
We are making progress! How much memory do...

We are making progress!

How much memory do you have on this Mac? I suggest using 85% of the maximum memory you have available with BBTools. You also need to specify "in1= and out1=" to go with...
Forum: Bioinformatics 02-06-2019, 08:31 AM
Replies: 347
Views: 185,363
Posted By GenoMax
On a Mac I tested this on nothing else was needed...

On a Mac I tested this on nothing else was needed to be done. What happens if you just run "bbmap.sh". Does that produce "in-line" bbmap help output?

Which Java version are you using on your Mac?
Forum: Bioinformatics 02-06-2019, 04:52 AM
Replies: 347
Views: 185,363
Posted By GenoMax
I am not sure why you are having this problem....

I am not sure why you are having this problem. All you should need to do is download BBMap software on your mac. Unarchive the tar-zipped file and then extend your path to include the "bbmap"...
Forum: Bioinformatics 01-06-2019, 05:25 PM
Replies: 347
Views: 185,363
Posted By GenoMax
@Seb: Brian does not seem to have time to respond...

@Seb: Brian does not seem to have time to respond to questions in this forum now a days but the different length of the adapters may have some bearing on this. Since the part you are looking for is...
Forum: Bioinformatics 12-20-2018, 04:05 AM
Replies: 347
Views: 185,363
Posted By GenoMax
@enma_ai: It is a bad idea to have spaces in your...

@enma_ai: It is a bad idea to have spaces in your file/directory names (even though your OS may allow it). I suggest the you change "NGS 10273-Raw" to "NGS_10273-Raw" and see if that fixes the error...
Forum: Bioinformatics 10-04-2018, 04:41 AM
Replies: 347
Views: 185,363
Posted By GenoMax
@FlySquirrelFly: It has become difficult to get a...

@FlySquirrelFly: It has become difficult to get a hold of Brian (due to his day job responsibilities) but I will flag your post for him to see if he can respond.

I recall from some past discussion...
Forum: Bioinformatics 07-19-2018, 03:57 AM
Replies: 347
Views: 185,363
Posted By GenoMax
@jsena33: You should take a look at UMI tools ...

@jsena33: You should take a look at UMI tools (https://github.com/CGATOxford/UMI-tools)for this type of application.
Forum: Bioinformatics 07-12-2018, 08:59 PM
Replies: 347
Views: 185,363
Posted By GenoMax
Have you looked at the in-line help for...

Have you looked at the in-line help for "splitnextera.sh"? The adapters for Mate Pair libraries are in the "adapters.fa" file so you should be able to trim them as usual...
Forum: Bioinformatics 06-13-2018, 04:56 AM
Replies: 347
Views: 185,363
Posted By GenoMax
No hyphens. Just tpe and tbo.

No hyphens. Just tpe and tbo.
Forum: Bioinformatics 06-12-2018, 06:24 PM
Replies: 347
Views: 185,363
Posted By GenoMax
@horvathdp: You can provide NEBnext primers...

@horvathdp: You can provide NEBnext primers (https://www.neb.com/-/media/catalog/datacards-or-manuals/manuale7335.pdf) in a separate file as multi-fasta sequence. Then use that file with bbduk.sh....
Forum: Bioinformatics 03-19-2018, 03:36 AM
Replies: 347
Views: 185,363
Posted By GenoMax
What OS are you using? Did you move any of the...

What OS are you using? Did you move any of the files around after you downloaded and uncompressed the software?

I am not sure where the WAYS=7 option is in README. You should be able to run bbduk...
Forum: Bioinformatics 03-09-2018, 08:13 AM
Replies: 347
Views: 185,363
Posted By GenoMax
@cb841011: Since this was also cross-posted and...

@cb841011: Since this was also cross-posted and discussed on Biostars I will add a reference to the thread here: https://www.biostars.org/p/302864/

You could always use a closely related grass...
Forum: Bioinformatics 03-08-2018, 04:00 PM
Replies: 347
Views: 185,363
Posted By GenoMax
You should use bbsplit for this purpose...

You should use bbsplit for this purpose (http://seqanswers.com/forums/showthread.php?t=41288). Provide the genome for your fungus alongside the plant and bin the reads.
Forum: Bioinformatics 02-26-2018, 01:15 PM
Replies: 347
Views: 185,363
Posted By GenoMax
That is a pretty old version of BBMap. I suggest...

That is a pretty old version of BBMap. I suggest that you start by upgrading to the latest first.

It seems unlikely but are the rest of the reads failing other limits you have set?
Forum: Bioinformatics 10-16-2017, 04:39 AM
Replies: 347
Views: 185,363
Posted By GenoMax
Not having reads in sync causes issues with...

Not having reads in sync causes issues with mapping with most aligners (you note that bwa is an exception). I assume only case where R2 would be eliminated (while R1 remains) would be if you were...
Forum: Bioinformatics 10-15-2017, 02:25 PM
Replies: 347
Views: 185,363
Posted By GenoMax
@Dario: Have you tried this with a file that has...

@Dario: Have you tried this with a file that has the (/1 of old Illumina style of 1:N:0 of new read headers)? Interleaved files may need those identifiers to be there. They can be added by...
Forum: Bioinformatics 09-28-2017, 10:13 AM
Replies: 347
Views: 185,363
Posted By GenoMax
"just assemble what you consider to be the...

"just assemble what you consider to be the background"

Assemble as?
Forum: Bioinformatics 07-20-2017, 06:49 AM
Replies: 347
Views: 185,363
Posted By GenoMax
Because your literal adapter is also matching the...

Because your literal adapter is also matching the beginning of the read entire sequence to the right is removed (ktrim=r). If you change the sequence at the beginning by one base you will see that...
Forum: Bioinformatics 06-30-2017, 07:57 AM
Replies: 347
Views: 185,363
Posted By GenoMax
You can use a standard unix loop to iterate over...

You can use a standard unix loop to iterate over all files, grab the file basenames and use them in individual bbmap tools.
Showing results 1 to 25 of 47

 


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