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Forum: Bioinformatics 11-19-2015, 01:08 AM
Replies: 1
Views: 2,503
Posted By maasha
Announcing: BioDSL - Bioinformatics Domain Specific Language

BioDSL (http://maasha.github.io/BioDSL/) (pronounced Biodiesel) is a Domain Specific Language for creating bioinformatic analysis workflows. A workflow may consist of several pipelines and each...
Forum: De novo discovery 06-25-2015, 04:56 AM
Replies: 7
Views: 5,164
Posted By maasha
I should say Biopieces (http://www.biopieces.org)...

I should say Biopieces (http://www.biopieces.org) is pretty nifty for this task:


https://code.google.com/p/biopieces/wiki/HowTo#Howto_analyze_assembled_contigs

You simply do:

read_fasta -i...
Forum: Illumina/Solexa 09-10-2014, 05:58 AM
Replies: 5
Views: 3,936
Posted By maasha
So how do you get the MiSeq to generate FASTQ...

So how do you get the MiSeq to generate FASTQ files including the indices so you may demultiplex manually?
Forum: Bioinformatics 04-09-2014, 04:35 AM
Replies: 4
Views: 1,667
Posted By maasha
Prodigal is really good. It's got a *meta*...

Prodigal is really good. It's got a *meta* switch.

http://prodigal.ornl.gov/
Forum: Bioinformatics 02-03-2014, 02:00 AM
Replies: 11
Views: 2,511
Posted By maasha
Jbrowse supports all sorts of custom track types....

Jbrowse supports all sorts of custom track types.


Martin
Forum: Bioinformatics 01-25-2014, 10:30 PM
Replies: 11
Views: 2,511
Posted By maasha
Btw, I posted this question some years ago: ...

Btw, I posted this question some years ago:

http://www.biostars.org/p/9168/

so also search!
Forum: Bioinformatics 01-25-2014, 10:20 PM
Replies: 11
Views: 2,511
Posted By maasha
Well, you need to find out what exactly you want...

Well, you need to find out what exactly you want from the genome browser. Then figure out if it can give you this, and finally, how.
Forum: Bioinformatics 01-25-2014, 10:10 PM
Replies: 11
Views: 2,511
Posted By maasha
Jbrowse is now quite mature and the gives the...

Jbrowse is now quite mature and the gives the best browsing experience IMHO. But the choice totally depends on what you actually need.
Forum: Bioinformatics 12-11-2013, 01:11 AM
Replies: 1
Views: 1,743
Posted By maasha
Have a look at get_seq from Biopieces...

Have a look at get_seq from Biopieces (www.biopieces.org):

https://code.google.com/p/biopieces/wiki/get_seq
Forum: Bioinformatics 12-11-2013, 01:10 AM
Replies: 5
Views: 4,271
Posted By maasha
Using Biopieces (www.biopieces.org): ...

Using Biopieces (www.biopieces.org):

Assembled contigs can be analyzed to get some stats using analyze_assembly. We include a filtering step to discard contigs shorter than 200 bases:
...
Forum: Bioinformatics 09-26-2013, 07:41 AM
Replies: 1
Views: 1,097
Posted By maasha
Honest question. Read this: ...

Honest question. Read this:

http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1002202
Forum: Bioinformatics 09-16-2013, 07:39 AM
Replies: 6
Views: 2,894
Posted By maasha
OK, another try with Biopieces - this time from...

OK, another try with Biopieces - this time from GenBank files ...

read_genbank -i test.gb -f gene | # read in genbank entries with gene feature key
add_ident -k SEQ_NAME | # add an identifier...
Forum: Bioinformatics 09-16-2013, 04:37 AM
Replies: 6
Views: 2,894
Posted By maasha
Let me see if I understand this correctly. You...

Let me see if I understand this correctly. You can use Biopieces (www.biopieces.org) like this (or modify a bit):

read_fasta -i genes.fna | # read in your sequences
split_seq -w 22 | # split the...
Forum: Bioinformatics 09-13-2013, 12:56 AM
Replies: 5
Views: 4,206
Posted By maasha
You can use Biopieces (www.biopieces.org): ...

You can use Biopieces (www.biopieces.org):


https://code.google.com/p/biopieces/wiki/HowTo#Howto_analyze_assembled_contigs
Forum: Bioinformatics 06-26-2013, 05:23 AM
Replies: 8
Views: 1,977
Posted By maasha
Biopieces -> www.biopieces.org

Biopieces -> www.biopieces.org
Forum: Bioinformatics 06-24-2013, 03:54 AM
Replies: 8
Views: 5,263
Posted By maasha
The CLC explanation is nice and crisp: ...

The CLC explanation is nice and crisp:

http://www.clcsupport.com/clcassemblycell/current/index.php?manual=How_it_works.html
Forum: Bioinformatics 05-08-2013, 08:08 AM
Replies: 9
Views: 12,087
Posted By maasha
Of cause Biopieces can do that. Check this out: ...

Of cause Biopieces can do that. Check this out:

https://code.google.com/p/biopieces/wiki/HowTo#Howto_get_some_basic_sequence_statistics
Forum: Bioinformatics 05-07-2013, 11:48 AM
Replies: 9
Views: 12,087
Posted By maasha
Biopieces reads gzipped files.

Biopieces reads gzipped files.
Forum: Bioinformatics 05-07-2013, 11:21 AM
Replies: 9
Views: 12,087
Posted By maasha
Biopieces (www.biopieces.org) have a bunch of...

Biopieces (www.biopieces.org) have a bunch of useful tools:

https://code.google.com/p/biopieces/wiki/HowTo#Quality_assurance_and_cleaning_NGS_data
Forum: Bioinformatics 04-22-2013, 01:17 AM
Replies: 2
Views: 1,029
Posted By maasha
In fact, Solexa and Illumina scores cover the...

In fact, Solexa and Illumina scores cover the whole of the printable ASCII alphabet (0-93) like Phred. However, mostly the scores are from 0-40, but with the new instruments you will often find...
Forum: Bioinformatics 03-29-2013, 11:48 AM
Replies: 3
Views: 2,601
Posted By maasha
This can also be done with Biopieces...

This can also be done with Biopieces (www.biopieces.org):

read_tab -i in.tab -k SEQ,COUNT | duplicate_record -k COUNT | add_ident -k SEQ_NAME -p Sample1_ | write_fasta -x
Forum: Bioinformatics 03-25-2013, 11:18 AM
Replies: 12
Views: 11,286
Posted By maasha
With Biopieces (www.biopieces.org) you can do it...

With Biopieces (www.biopieces.org) you can do it in two steps where you first find the mean score per sequence entry and then the overall mean score:

read_fastq -i test.fq | mean_scores |...
Forum: Bioinformatics 03-19-2013, 02:25 PM
Replies: 3
Views: 3,278
Posted By maasha
Maybe, just maybe, you can do it with Artemis...

Maybe, just maybe, you can do it with Artemis from Sanger
Forum: Bioinformatics 03-12-2013, 02:06 AM
Replies: 14
Views: 2,915
Posted By maasha
@yaximik New questions in new threads. Do...

@yaximik

New questions in new threads. Do your homework first:

read this:

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002202

and then
Forum: Bioinformatics 03-06-2013, 12:50 AM
Replies: 9
Views: 4,739
Posted By maasha
Thanks yifangt, I will post this to the Biopieces...

Thanks yifangt, I will post this to the Biopieces Google Group and answer there.
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