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Search: Posts Made By: GenoMax
Forum: Bioinformatics 10-25-2021, 06:35 AM
Replies: 3
Views: 615
Posted By GenoMax
If you need full length perfect alignments in...

If you need full length perfect alignments in your final file then I suggest that you try "perfectmode=t minid=1 mappedonly=t" options. If your reads are longer than 150 bp then you may need to...
Forum: Bioinformatics 10-25-2021, 05:13 AM
Replies: 3
Views: 615
Posted By GenoMax
Do you have 20 cores available on the machine for...

Do you have 20 cores available on the machine for BBMap to use. What happens if you assign fewer cores? Starting with 8 would be a good number.
Forum: Bioinformatics 10-15-2021, 12:40 PM
Replies: 1
Views: 703
Posted By GenoMax
You can align your contigs to the genome sequence...

You can align your contigs to the genome sequence and check. A program like Mauve (http://darlinglab.org/mauve/mauve.html) also comes in handy to check the coverage visually.
Forum: Bioinformatics 10-13-2021, 12:47 PM
Replies: 347
Views: 189,582
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, 04:13 AM
Replies: 347
Views: 189,582
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 09-27-2021, 07:14 AM
Replies: 3
Views: 965
Posted By GenoMax
Python is generally symlinked to python v.2.x....

Python is generally symlinked to python v.2.x. Can you explicitly try `python3`?
Forum: Metagenomics 09-24-2021, 11:59 AM
Replies: 3
Views: 1,424
Posted By GenoMax
See:...

See: http://seqanswers.com/forums/showthread.php?t=41288
Forum: Bioinformatics 09-23-2021, 03:09 PM
Replies: 1
Views: 985
Posted By GenoMax
Is there a specific reason you converted these...

Is there a specific reason you converted these reads to fasta format? If this is data from SRA then you should be able to map the fastq reads directly.

You may be getting secondary alignments and...
Forum: Bioinformatics 09-23-2021, 03:06 PM
Replies: 693
Views: 249,812
Posted By GenoMax
You should be able to use covstats=<file> ...

You should be able to use covstats=<file> Per-scaffold coverage info. for each of your commands. You can also capture the stderr/out to a file to get statistics....
Forum: Metagenomics 09-23-2021, 03:03 PM
Replies: 3
Views: 1,424
Posted By GenoMax
You should use a different program for this...

You should use a different program for this purpose. Look up "bbsplit.sh". BBDuk is not the right program for this application.
Forum: Bioinformatics 09-21-2021, 06:24 AM
Replies: 1
Views: 831
Posted By GenoMax
You could use "minimap2" to align against the...

You could use "minimap2" to align against the human genome. That said you will need to be judicious about results as you determine what is "human" contamination. Depending on the genomes you are...
Forum: Bioinformatics 09-18-2021, 07:00 AM
Replies: 6
Views: 1,043
Posted By GenoMax
Brian's email address is in the inline help for...

Brian's email address is in the inline help for bbmap programs. Just run `bbmap.sh` and look through the help.

It may be by design then. Error correction requires keeping large amount of sequence...
Forum: Bioinformatics 09-17-2021, 11:58 AM
Replies: 6
Views: 1,043
Posted By GenoMax
I may have bad news. All bbmap tools are supposed...

I may have bad news. All bbmap tools are supposed to be able to accept input from STDIN but it appears that "tadpole.sh" may be an exception. This is something Brian (author of BBMap may know the...
Forum: Illumina/Solexa 09-16-2021, 03:03 PM
Replies: 2
Views: 957
Posted By GenoMax
NovaSeq may be an overkill unless you have...

NovaSeq may be an overkill unless you have multiple bacterial genomes you are planning to sequence at the same time. This paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706130/) is a good read...
Forum: Bioinformatics 09-16-2021, 01:40 PM
Replies: 6
Views: 1,043
Posted By GenoMax
You should be able to pass fastq to all BBtools....

You should be able to pass fastq to all BBtools. Use in=stdin.fq when you are doing that.
Forum: Bioinformatics 09-11-2021, 05:40 AM
Replies: 693
Views: 249,812
Posted By GenoMax
@mewu3: Since paired-end reads are aligned...

@mewu3: Since paired-end reads are aligned together you should use a single "out=output.sam". If you wanted to capture unmapped reads into separate files then you would want to do that as...
Forum: Bioinformatics 09-07-2021, 09:30 AM
Replies: 693
Views: 249,812
Posted By GenoMax
@mewu3: Unfortunately it can't. You will need to...

@mewu3: Unfortunately it can't. You will need to restart the job.
Forum: Bioinformatics 08-14-2021, 03:51 PM
Replies: 57
Views: 55,946
Posted By GenoMax
@Sean Depending on size of your dataset 21G...

@Sean Depending on size of your dataset 21G memory may not be enough.
Forum: Illumina/Solexa 08-04-2021, 07:53 AM
Replies: 6
Views: 1,374
Posted By GenoMax
You should be able to recover the data for...

You should be able to recover the data for 270-odd cycles and then take a look at it. phiX data should be in there. This may need to be done offline using bcl2fastq on the command line. Not sure if...
Forum: Illumina/Solexa 08-04-2021, 05:07 AM
Replies: 6
Views: 1,374
Posted By GenoMax
Then you have no option but to try another run....

Then you have no option but to try another run. What % of phiX was used for first run. Did that data look ok?
Forum: Illumina/Solexa 08-04-2021, 04:26 AM
Replies: 6
Views: 1,374
Posted By GenoMax
You should contact Illumina tech support so they...

You should contact Illumina tech support so they can look at the sequencer/run remotely to diagnose the problem. It could be an instrument blip but if there was a problem they can identify it.
Forum: Bioinformatics 08-03-2021, 02:08 PM
Replies: 57
Views: 55,946
Posted By GenoMax
Yes BBNorm works with paired-end files. If you...

Yes BBNorm works with paired-end files. If you have data that ran over multiple lanes then it would be fine to concatenate the reads in identical order for R1/R2 data.
Forum: Bioinformatics 07-23-2021, 07:49 AM
Replies: 3
Views: 1,363
Posted By GenoMax
As I said before as long as the files are...

As I said before as long as the files are concatenated in same order AND they had the same number of reads in sync across R1/R2 files to begin with this should work without any problems. If things...
Forum: Bioinformatics 07-02-2021, 08:15 AM
Replies: 174
Views: 62,615
Posted By GenoMax
Download pre-compiled binary for macOS from here...

Download pre-compiled binary for macOS from here (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.4/bowtie2-2.4.4-macos-x86_64.zip/download).

Consider using "conda" to install these...
Forum: Illumina/Solexa 07-01-2021, 10:11 AM
Replies: 2
Views: 1,518
Posted By GenoMax
If possible have Illumina tech support have a...

If possible have Illumina tech support have a look at this run. Something could be wrong with it. Poly-G generally means there was no signal for 1- and 2-color runs. It is theoretically possible that...
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