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Forum: Bioinformatics 11-19-2013, 08:08 PM
Replies: 20
Views: 11,395
Posted By Bgansw
Hi Gringer, Thanx f the tip. I've gone over...

Hi Gringer,

Thanx f the tip. I've gone over all the file names, and have changed the 53340.5.fna to 533240.5.fa but I'm still getting the same error. Does this command work well for you? I'm...
Forum: Bioinformatics 11-19-2013, 05:54 PM
Replies: 20
Views: 11,395
Posted By Bgansw
Hello Jimmybee and Gringer, Thanx for your...

Hello Jimmybee and Gringer,

Thanx for your guidance with this.

I've been trying the commands (samtools, bcftools).. and I'm getting an error:

bgansw@BioinfoSecond:~/bwa/samtools-0.1.18$...
Forum: Bioinformatics 11-04-2013, 07:46 PM
Replies: 20
Views: 11,395
Posted By Bgansw
Illumina - mapping genome on reference - how to extract assembly?

Hello,

I'm having trouble extracting assembled reads after using soapaligner.

I mapped my raw reads to my reference genome using soap aligner, how do I then extract the assembly and submit for...
Forum: Bioinformatics 11-04-2013, 07:36 PM
Replies: 2
Views: 1,481
Posted By Bgansw
Illumina nextra sequencing

Hello,

I'm trying to assemble my illumina sequenced- cyanobacterial genome.. using soapdenovo and velvet, but I'm getting extremely low N50's like less than a 1000. I've never faced such a...
Forum: Bioinformatics 11-11-2012, 07:18 PM
Replies: 0
Views: 1,448
Posted By Bgansw
Copy number variation and synteny mapping for bacterial genomes

Hello,

I have three bacterial genomes (~ 4 Mb), all strains of the same species. One has already been published and will serve as a reference genome for my study.

How do I find the copy number...
Forum: Illumina/Solexa 11-08-2012, 08:43 PM
Replies: 0
Views: 1,507
Posted By Bgansw
Hiseq reads -assembly n mapping on a reference genome

Hi,

Background: Got 5 genomes sequenced with the GA2, assembled n annotated them denovo using soapdenovo, velvet.. also mapped them on to a reference using soap aligner.. no problem. Then got...
Forum: Bioinformatics 11-04-2012, 06:49 PM
Replies: 2
Views: 1,499
Posted By Bgansw
Fungal genome Annotation

Hello,

I'm new to genome assembly.

I've got fungal genome, that I've assembled using Velvet and Soap denovo. I have used Genemark for gene calling. Now how do I annotate it?

Are there any...
Forum: Bioinformatics 02-22-2012, 08:21 PM
Replies: 23
Views: 23,264
Posted By Bgansw
Hi Swarnes2, I was able to convert the...

Hi Swarnes2,

I was able to convert the unmapped.bam files to fastq and then assemble them in velvet.

I'm annotating them now.

Thank you. I guess I'm sorted for now.

Again, thank you very...
Forum: Bioinformatics 02-22-2012, 06:37 PM
Replies: 23
Views: 23,264
Posted By Bgansw
extract unmapped reads from bwa - convert to fastq

Hi Swarnes2,

Thank you very very much for your detailed post. Since I'm a newbie, the post was direct, easy to understand and very helpful. Thank you very very much. I'm very grateful!

I ran...
Forum: Bioinformatics 02-21-2012, 04:43 PM
Replies: 23
Views: 23,264
Posted By Bgansw
Hi swbarnes2, I ran bwa using the aln...

Hi swbarnes2,

I ran bwa using the aln parameter, instead of the bwasw, but am not sure that its worked. The output .sam file is only 4K, while the bwasw output file was 796K. Additionally, the...
Forum: Bioinformatics 02-21-2012, 03:21 PM
Replies: 23
Views: 23,264
Posted By Bgansw
Hi Freeseek, I inputted my faq file in the...

Hi Freeseek,

I inputted my faq file in the file to patch. That gave me .fastq.orig file and .fastq.rej

Copy pasting the .orig file

bgansw:~/bwa$ head 6_combined_paired.faq.orig...
Forum: Bioinformatics 02-21-2012, 03:12 PM
Replies: 23
Views: 23,264
Posted By Bgansw
Unmapped reads bwasw + patch

Hi Freeseek,



I'm trying to align my sample illumina bacterial genome to an already published reference bacterial genome. The aim is to find out what genes are present in my sample genome, but...
Forum: Bioinformatics 02-20-2012, 04:00 PM
Replies: 2
Views: 2,759
Posted By Bgansw
Thank you Genomax. I've been able to...

Thank you Genomax.

I've been able to successfully extract the mapped and unmapped reads, thanks to your advice. I did have a query though, and I've posted it along the thread you'd specified in...
Forum: Bioinformatics 02-20-2012, 03:57 PM
Replies: 11
Views: 37,875
Posted By Bgansw
extract unmapped reads

Hello Alex,

I wanted to confirm if I'm interpreting my results correctly.I'm trying to align my sample illumina bacterial genome to an already published reference bacterial genome. The aim is to...
Forum: Bioinformatics 02-19-2012, 08:24 PM
Replies: 2
Views: 2,759
Posted By Bgansw
bwasw

Hello,

I'm new to bioinformatics, and need help with bwasw.

I'm trying to align my sample illumina bacterial genome to an already published reference bacterial genome. The aim is to find out...
Forum: Bioinformatics 02-02-2012, 05:10 PM
Replies: 0
Views: 1,453
Posted By Bgansw
RATT annotation tool help

Hello,

I'm new to bioinformatics and am trying to use the RATT annotation tool to transfer annotation from an already sequenced bacterial strain to another very closely related one.

RATT has...
Forum: Bioinformatics 12-27-2011, 01:17 AM
Replies: 18
Views: 6,752
Posted By Bgansw
Tried A5 pipeline on Hiseq raw data:

Hi Koadman,

My apologies for the delay in getting back to you. Had to go overseas!

I tried the new A5 pipeline, and although it worked, I'm having the same problem, that I have with the other...
Forum: Bioinformatics 12-24-2011, 08:13 AM
Replies: 1
Views: 1,554
Posted By Bgansw
Need help using RATT

Hi,

I'm new to RATT. I've set it up as specified in the documentation (http://ratt.sourceforge.net/documentation.html).
This is the error msg I'm getting on running it.

Any help on this would...
Forum: Bioinformatics 12-05-2011, 06:52 PM
Replies: 18
Views: 6,752
Posted By Bgansw
Hi Koadman, Am getting this error message,...

Hi Koadman,

Am getting this error message, with the pipeline. I suspect that its because the new Hiseq data has been processed by casava 1.8, and generates reads in sanger format (also known as...
Forum: Bioinformatics 12-04-2011, 08:07 PM
Replies: 18
Views: 6,752
Posted By Bgansw
Hi Koadman, The A5 pipeline is running on...

Hi Koadman,

The A5 pipeline is running on our cluster right now. So far all good!

I'll keep you updated with the results. Hopefully, it'll all run smoothly..

Thanx a ton.
Forum: Bioinformatics 11-30-2011, 03:22 PM
Replies: 18
Views: 6,752
Posted By Bgansw
Hi Koadman, I've installed the A5 pipeline...

Hi Koadman,

I've installed the A5 pipeline in my bin folder n have tried to install it.

The a5_pipeline.pl is blinking, and its highlighted in red n not working.

How do I rectify this?
Forum: Bioinformatics 11-29-2011, 07:38 PM
Replies: 18
Views: 6,752
Posted By Bgansw
Thank you Koadman and vamosia. Yes, I'll reduce...

Thank you Koadman and vamosia. Yes, I'll reduce the dept and try again.

@Koadman: I've downloaded your A5 pipe line. Thanks. I'll keep you'll updated with the result.

Bgansw
Forum: Bioinformatics 11-29-2011, 03:02 PM
Replies: 18
Views: 6,752
Posted By Bgansw
Genome assembly -hiseq illumina data

Hi,

I'm new to genome assembly, and am having problems.

I will be grateful for tips on how to assemble a bacterial genome.

I have 100bp hiseq illumina data. Genome size is ~4MB.

I have...
Forum: Bioinformatics 11-15-2011, 04:28 PM
Replies: 0
Views: 1,994
Posted By Bgansw
Bacterial genome data from Hiseq - Query

Hello,

I'm trying to assemble a bacterial genome ~4Mb, and am facing an unusual problem.

While the Kmerfreq script gives me an appropriate estimation of genome size (only in the manual...
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