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Forum: De novo discovery 08-13-2019, 04:57 PM
Replies: 7
Views: 269
Posted By GenoMax
See this thread: https://www.biostars.org/p/78315/

See this thread: https://www.biostars.org/p/78315/
Forum: De novo discovery 08-13-2019, 03:55 PM
Replies: 7
Views: 269
Posted By GenoMax
I suggest you give "tadpole.sh" from BBMap suite...

I suggest you give "tadpole.sh" from BBMap suite a try. It works well with small genomes. Tadpole guide is here (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/tadpole-guide/).

If...
Forum: RNA Sequencing 08-08-2019, 03:17 AM
Replies: 1
Views: 222
Posted By GenoMax
I assume you are referring to adapter sequences....

I assume you are referring to adapter sequences. Strictly speaking you don't need to since most modern aligners will soft clip them.

That said, it can be a good practice to scan and trim your...
Forum: Bioinformatics 08-06-2019, 09:03 AM
Replies: 3
Views: 263
Posted By GenoMax
@Ben: MiSeq nano flowcells produce a small amount...

@Ben: MiSeq nano flowcells produce a small amount of data and can run astonishingly quickly. That 4 h figure is for one of these FC with a short 50 cycle run. These FC only produce about 1-1.5M reads...
Forum: Bioinformatics 08-05-2019, 10:28 AM
Replies: 238
Views: 80,933
Posted By GenoMax
BBMap is not designed to work with protein data....

BBMap is not designed to work with protein data. You will have to find a different tool.

Take a look at blat from UCSC's Jim Kent. That should produce the stats in parse-able tab-delimited...
Forum: Ion Torrent 08-02-2019, 08:41 AM
Replies: 16
Views: 879
Posted By GenoMax
@Haiqu: You should clarify if you are looking at...

@Haiqu: You should clarify if you are looking at Ion as a hobbyist (outside of a research institution) i.e. for DIY use.
Forum: Bioinformatics 07-27-2019, 01:15 PM
Replies: 104
Views: 30,048
Posted By GenoMax
Instead of trying to extend the reads use tadpole...

Instead of trying to extend the reads use tadpole in assembly mode. I linked a guide for how to use "tadpole" and its modes in my last comment.

You may have too much coverage for small genomes...
Forum: Bioinformatics 07-27-2019, 06:53 AM
Replies: 104
Views: 30,048
Posted By GenoMax
Is this data in addition to contigs file or are...

Is this data in addition to contigs file or are they reads that were used to make the contig assembly?

Take a look at this tadpole usage guide...
Forum: Bioinformatics 07-21-2019, 04:02 PM
Replies: 4
Views: 494
Posted By GenoMax
You can certainly use Brian's recommendation...

You can certainly use Brian's recommendation above. If you wish to find out how many reads actually map to those individual references (e.g. rRNA, mito etc) then using bbsplit.sh would be useful...
Forum: Bioinformatics 07-21-2019, 12:16 PM
Replies: 8
Views: 759
Posted By GenoMax
At least one tool from BBTools suite is...

At least one tool from BBTools suite is published. Here is the paper for BBMerge (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185056).

It is my understanding that BBTools...
Forum: Bioinformatics 07-17-2019, 03:04 AM
Replies: 4
Views: 494
Posted By GenoMax
There is no pipeline needed. You can provide...

There is no pipeline needed. You can provide contaminants you want to remove as fasta sequence in a file.

While you could use `bbduk.sh` you may want to use `bbsplit.sh` in this case to bin the...
Forum: Bioinformatics 07-13-2019, 07:30 AM
Replies: 10
Views: 770
Posted By GenoMax
@SDPA_Pet: Your sequencing facility may have...

@SDPA_Pet: Your sequencing facility may have simply run 2x150 sequencing by mistake if you are sure the reads have not been trimmed.

You should be able to ask them to re-sequence the sample 2x300,...
Forum: Bioinformatics 07-12-2019, 03:24 AM
Replies: 10
Views: 770
Posted By GenoMax
What does that mean? Is the data pretrimmed,...

What does that mean? Is the data pretrimmed, which is why you have much shorter reads than expected? If all reads are 150 bp, sequencing facility may have made an error with run setup, if you had...
Forum: General 07-11-2019, 04:25 AM
Replies: 4
Views: 689
Posted By GenoMax
Do you know about 10x genomics technology? ...

Do you know about 10x genomics technology? https://www.10xgenomics.com/technology/
This may be a good topic to read up on and present.

stLFR is also similar/interesting tech. See this paper ...
Forum: Bioinformatics 07-10-2019, 03:40 AM
Replies: 238
Views: 80,933
Posted By GenoMax
Unfortunately Brian would be the only person who...

Unfortunately Brian would be the only person who can provide an authoritative answer and he no longer participates on this forum. You may want to try emailing him with your question directly.
...
Forum: Bioinformatics 07-09-2019, 09:52 AM
Replies: 238
Views: 80,933
Posted By GenoMax
Metagenome option is supposed to take in multiple...

Metagenome option is supposed to take in multiple (genome) sequences to generate an artificial metagenomic dataset.

BBMap writes stats to STDERR by default. So you can capture that.
Forum: Bioinformatics 07-09-2019, 03:25 AM
Replies: 238
Views: 80,933
Posted By GenoMax
Since you asked for 30K reads you got 30K...

Since you asked for 30K reads you got 30K paired-end reads.

I would sugegst trying without the metagenome=t option for a single small input fasta. If you do have the entire genome then use that in...
Forum: RNA Sequencing 07-08-2019, 04:02 AM
Replies: 1
Views: 305
Posted By GenoMax
Technical replicates can be merged for downstream...

Technical replicates can be merged for downstream analysis. Only biological replicates are useful for meaningful statistical analysis.
Forum: Illumina/Solexa 07-02-2019, 03:01 AM
Replies: 1
Views: 435
Posted By GenoMax
If you only plan to do one or two runs a month it...

If you only plan to do one or two runs a month it may not be worth your time. Sequencers have fine capillaries, complex electronics and are generally happier when run reasonably continuously. The...
Forum: Bioinformatics 06-26-2019, 06:32 AM
Replies: 238
Views: 80,933
Posted By GenoMax
@Noobie: I don't think so. You will have to do...

@Noobie: I don't think so. You will have to do them independently. What is the use case here, if I may ask?
Forum: Bioinformatics 06-21-2019, 10:05 AM
Replies: 2
Views: 459
Posted By GenoMax
Cross posted and answered on Biostars:...

Cross posted and answered on Biostars: https://www.biostars.org/p/385930/
Forum: Bioinformatics 06-18-2019, 05:44 AM
Replies: 6
Views: 464
Posted By GenoMax
The problem is there is no formal definition of...

The problem is there is no formal definition of fasta header. It can be anything following a ">" sign and that is what makes this problemmatic.

BBMap is actually being very flexible by allowing...
Forum: Bioinformatics 06-17-2019, 11:57 AM
Replies: 6
Views: 464
Posted By GenoMax
Since you have those numbers duplicated in your...

Since you have those numbers duplicated in your reference file fasta headers those are showing up in your alignments. BBMap is one of few aligners that passes along the entire string (including...
Forum: Bioinformatics 06-17-2019, 09:41 AM
Replies: 6
Views: 464
Posted By GenoMax
Show us the headers in your reference file. grep...

Show us the headers in your reference file. grep "^>" your_ref.fa

BTW: I don't see a "path=" or "ref=" directive in your map command above.
Forum: Bioinformatics 06-15-2019, 04:32 PM
Replies: 5
Views: 622
Posted By GenoMax
Possibly. You will have to play with parameters...

Possibly. You will have to play with parameters for bbduk.sh. "0" should be easy to get.
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