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Search: Posts Made By: GenoMax
Forum: General 09-17-2019, 03:03 PM
Replies: 14
Views: 875
Posted By GenoMax
Then we have been on wrong track all along. You...

Then we have been on wrong track all along. You should have said you need a consensus fasta file from the BAM alignment.

What you need is: https://www.biostars.org/p/367960/

I had posted this...
Forum: General 09-17-2019, 12:00 PM
Replies: 14
Views: 875
Posted By GenoMax
Output fasta reads were interleaved (put in one...

Output fasta reads were interleaved (put in one file) since you had paired-end reads to begin with. To separate them into two files you should use the command below.


for i in *.fa; do...
Forum: Bioinformatics 09-16-2019, 09:37 AM
Replies: 1
Views: 191
Posted By GenoMax
Cross-posted on biostars:...

Cross-posted on biostars: https://www.biostars.org/p/398986/
Forum: General 09-12-2019, 08:23 AM
Replies: 14
Views: 875
Posted By GenoMax
Good catch SNPsaurus. I have updated my original...

Good catch SNPsaurus. I have updated my original command. There was an additional ".bam" in there.

@Manuelly: Use for i in *.bam; do reformat.sh in=$i out=${i}.fa; done

If you are trying to...
Forum: General 09-10-2019, 08:57 AM
Replies: 2
Views: 279
Posted By GenoMax
You need to provide more information about what...

You need to provide more information about what software you are running, how you are running it. Is it custom code you wrote or a package that is available on web?
Forum: Bioinformatics 09-09-2019, 07:57 PM
Replies: 330
Views: 111,218
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 08-29-2019, 11:05 PM
Replies: 2
Views: 366
Posted By GenoMax
Have you tried to see where (96-95-29.4) reads...

Have you tried to see where (96-95-29.4) reads are aligning (since they are not aligning to transcripts)? Does your data have rRNA present? Inspecting the resulting BAM using IGV would be a great...
Forum: General 08-28-2019, 08:30 AM
Replies: 14
Views: 875
Posted By GenoMax
Yes you can convert multiple files at once. If...

Yes you can convert multiple files at once. If your data came from paired-end reads then be aware that the "out=" files will contain data in interleaved format. You will need to separate R1/R2 reads....
Forum: General 08-27-2019, 03:52 PM
Replies: 14
Views: 875
Posted By GenoMax
Use reformat.sh from BBMap suite. Take a look at...

Use reformat.sh from BBMap suite. Take a look at BAM processing options in in-line help to decide if you want to keep primary reads etc.

for i in *.bam; do reformat.sh in=${i} out=${i}.fa...
Forum: Bioinformatics 08-22-2019, 01:43 PM
Replies: 6
Views: 465
Posted By GenoMax
You likely have a broken install then. Is...

You likely have a broken install then. Is entrezdirect supported on cygwin? If you have Windows 10 then you should use WSL instead.
Forum: Bioinformatics 08-22-2019, 01:34 PM
Replies: 6
Views: 465
Posted By GenoMax
Do you get something back with just first part?...

Do you get something back with just first part? An API key is only needed if you are going to run multiple entrezdirect commands over a period of time.

esearch -db pubmed -query "Roe B"
...
Forum: Bioinformatics 08-22-2019, 01:11 PM
Replies: 6
Views: 465
Posted By GenoMax
Break your search into smaller chunks. Make sure...

Break your search into smaller chunks. Make sure you are signed-up for and are using NCBI_API_KEY.
Forum: Illumina/Solexa 08-22-2019, 12:59 PM
Replies: 1
Views: 291
Posted By GenoMax
I don't immediately recall if we have done one on...

I don't immediately recall if we have done one on NovaSeq but have done so on patterned FC on HiSeq 4000. As long as you keep in mind that the quality scores are not properly calibrated until after...
Forum: Bioinformatics 08-22-2019, 01:34 AM
Replies: 240
Views: 83,851
Posted By GenoMax
@darthsequencer: You can use kmercountexact.sh...

@darthsequencer: You can use kmercountexact.sh from BBMap suite.
Forum: De novo discovery 08-13-2019, 04:57 PM
Replies: 7
Views: 759
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: 759
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: 438
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: 475
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: 240
Views: 83,851
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: 19
Views: 1,864
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: 31,129
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: 31,129
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: 658
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: 1,070
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: 658
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...
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