SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 54
Search took 0.01 seconds.
Search: Posts Made By: fahmida
Forum: Bioinformatics 02-18-2017, 11:59 AM
Replies: 4
Views: 3,384
Posted By fahmida
Typically due to high error rate you have to...

Typically due to high error rate you have to correct your nanopore reads by more accurate short reads from e.g. illumina. There are several methods to do that. Then you can use something like SSPACE...
Forum: Bioinformatics 12-05-2016, 12:49 PM
Replies: 1
Views: 1,458
Posted By fahmida
You may have to do some filtering/pre-processing...

You may have to do some filtering/pre-processing etc. if you are using this script:
http://seqanswers.com/forums/showthread.php?t=20508
Details are there.
Forum: Bioinformatics 12-03-2016, 06:36 AM
Replies: 4
Views: 1,733
Posted By fahmida
You may try Quast: ...

You may try Quast:
http://bioinf.spbau.ru/en/quast
Forum: Bioinformatics 04-25-2016, 03:15 PM
Replies: 3
Views: 1,513
Posted By fahmida
Agree with SamCurt. You can quantify the...

Agree with SamCurt. You can quantify the expression level of genes for two samples, however, you do not have any statistical power to reliably estimate the differential expression.
Forum: Bioinformatics 03-08-2016, 01:10 PM
Replies: 252
Views: 105,649
Posted By fahmida
Please see the response of 'El Crazy Xabi' above....

Please see the response of 'El Crazy Xabi' above.
Either use -x = 0 or use an older version of SSPACE.
Forum: Bioinformatics 02-03-2016, 01:18 PM
Replies: 2
Views: 2,041
Posted By fahmida
Have you tried QUAST? ...

Have you tried QUAST?
http://bioinf.spbau.ru/quast
Forum: Bioinformatics 10-12-2015, 08:45 PM
Replies: 104
Views: 39,115
Posted By fahmida
Hi Brian, It seems like a powerful addition...

Hi Brian,

It seems like a powerful addition to BBTools.
Is it possible to use Tadpole for PacBio data (with accompanying illumina data).

Regards.
Forum: Bioinformatics 08-12-2015, 04:50 PM
Replies: 2
Views: 2,816
Posted By fahmida
I think the issue was with previous versions of...

I think the issue was with previous versions of RECON.
Current updated version (v1.08) as described in:
http://www.repeatmasker.org/RepeatModeler.html
and is available in:...
Forum: Bioinformatics 07-12-2015, 03:37 PM
Replies: 12
Views: 5,282
Posted By fahmida
Sometime ago I've faced similar issues and after...

Sometime ago I've faced similar issues and after searching into ALLPATHS forums etc I found the suggestion: increase the value of FF_MAX_STRETCH parameter of RunAllPathsLG pipeline, which worked for...
Forum: Bioinformatics 06-09-2015, 03:00 PM
Replies: 4
Views: 2,717
Posted By fahmida
You may have a look into: ...

You may have a look into:
http://kofler.or.at/bioinformatics/SciRoKo/index.html
It's fast and easy to use.
Forum: Bioinformatics 05-27-2015, 03:18 PM
Replies: 5
Views: 2,820
Posted By fahmida
I also agree with Torsten and Colin. Augustus is...

I also agree with Torsten and Colin. Augustus is much easier to deal with.
Forum: Bioinformatics 03-20-2015, 01:17 AM
Replies: 8
Views: 1,886
Posted By fahmida
You can start with SSPACE. ...

You can start with SSPACE.
http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE
Forum: Bioinformatics 03-17-2015, 05:57 PM
Replies: 8
Views: 1,886
Posted By fahmida
Allpaths-LG is a good option if you have enough...

Allpaths-LG is a good option if you have enough RAM and CPUs. Also I wonder whether one of your PE libraries are overlapping i.e. from Allpaths-LG doc "average separation size must be slightly less...
Forum: Bioinformatics 03-06-2015, 06:43 PM
Replies: 252
Views: 105,649
Posted By fahmida
-x 1 worked fine with previous releases of SSPACE...

-x 1 worked fine with previous releases of SSPACE (from my own experience).
I am sure Marten is investigating the issue with the current version.
Forum: Bioinformatics 03-05-2015, 01:47 PM
Replies: 5
Views: 2,669
Posted By fahmida
Have a look into: http://qiime.org/ and ...

Have a look into:
http://qiime.org/
and
http://www.mothur.org/

Reference to databases:
http://qiime.org/home_static/dataFiles.html

This should get you started.
Forum: Bioinformatics 03-05-2015, 01:38 PM
Replies: 252
Views: 105,649
Posted By fahmida
Hi, For the above bwa and bowtie issues, it...

Hi,

For the above bwa and bowtie issues, it seems to work fine with the default contig extension parameter i.e. -x 0.
The problem occurs if I want to extend the contigs during scaffolding i.e. -x...
Forum: Bioinformatics 03-01-2015, 03:39 PM
Replies: 2
Views: 2,816
Posted By fahmida
RepeatModeler Error (eleredef failed. Exit code 768)

Hi,

I am stuck with RepeatModeler with error:
eleredef failed. Exit code 768

Here is the full log:

/software/RepeatModeler/RepeatModeler -database test.txt -pa 10
RepeatModeler Version...
Forum: Bioinformatics 02-23-2015, 05:37 PM
Replies: 252
Views: 105,649
Posted By fahmida
Hi Boetsie, As jpummil mentioned above I am...

Hi Boetsie,

As jpummil mentioned above I am also encountering similar error with SSPACE Standard v3.0.
I ran the following command with BOWTIE and BWA:...
Forum: Bioinformatics 11-05-2014, 03:35 PM
Replies: 12
Views: 4,799
Posted By fahmida
I am also having the same error "[err] All reads...

I am also having the same error "[err] All reads within a file must be the same length". I am not sure I understand the rationale behind this. Once the raw reads e.g. 100 or 150nt length are trimmed...
Forum: Bioinformatics 11-05-2014, 03:22 PM
Replies: 5
Views: 1,868
Posted By fahmida
Good luck with Prokka installation. Though it is...

Good luck with Prokka installation. Though it is a handy tool, it has a scary list of requirements and I couldn't get over it in three attempts so far and gave up for now.
Forum: Bioinformatics 09-24-2014, 03:22 PM
Replies: 4
Views: 1,436
Posted By fahmida
@Brian: I really appreciate your comprehensive...

@Brian: I really appreciate your comprehensive reply. I am involved in de novo assembly of moderate sized plant genomes without any close reference. Dealing with massive volumes of data (multiple PE...
Forum: Bioinformatics 09-23-2014, 10:55 PM
Replies: 4
Views: 1,436
Posted By fahmida
Multiple read QC steps (trimming, filtering etc) in one go ... what's the best way?

Hi,

I know there are many versatile tools (bbduck, trimmomatic etc. to name a a few) that can trim low quality bases, adapters etc. I wonder what would be the best way to do the followings with a...
Forum: Bioinformatics 09-15-2014, 08:41 PM
Replies: 4
Views: 3,506
Posted By fahmida
You need to consider several things. Is it a...

You need to consider several things.
Is it a plant or animal genome? Do you have a reference?
How complex is the genome i.e ploidy etc?
I don't think mate pair alone can do much. Also you just...
Forum: Bioinformatics 09-10-2014, 11:00 PM
Replies: 3
Views: 1,104
Posted By fahmida
The following should get you started: ...

The following should get you started:

http://www.arb-silva.de/
http://greengenes.secondgenome.com/downloads
Forum: Bioinformatics 08-26-2014, 03:52 PM
Replies: 22
Views: 4,896
Posted By fahmida
The choice of hardware and software will depend a...

The choice of hardware and software will depend a lot on the problem and nature of data you are working with. For me I always want the option of customizing the environment: from OS to any open...
Showing results 1 to 25 of 54

 


All times are GMT -8. The time now is 06:59 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO