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Forum: Metagenomics 06-28-2016, 02:23 AM
Replies: 7
Views: 1,839
Posted By Krish_143
Hi Julia_m, Is that Genomic data or RNAseq -...

Hi Julia_m,

Is that Genomic data or RNAseq - transcriptomic data. Okay !

If it was not aligning that could mean.. paired read was not found in one of the other file.

Probably you might...
Forum: Bioinformatics 06-28-2016, 01:33 AM
Replies: 0
Views: 660
Posted By Krish_143
finding the Insertion Sequences (IS elements) in draft genomes.

Hi,

Is there any tool or a simple method ??

How to detect the IS elements from the draft genome (bacteria).
I have tried ISsaga (using ISfinder) and ISQuest.

ISsaga annotate the draft...
Forum: Bioinformatics 02-27-2014, 10:30 PM
Replies: 11
Views: 1,958
Posted By Krish_143
You can download at ...

You can download at
https://bitbucket.org/feeldead/gfold/downloads

For downlading to linux :

wget https://bitbucket.org/feeldead/gfold/downloads/gfold.V1.1.1.tar.gz

Check Readme and...
Forum: Bioinformatics 02-27-2014, 12:07 PM
Replies: 11
Views: 1,958
Posted By Krish_143
When we have no replicates.. then i suggest u to...

When we have no replicates.. then i suggest u to try Gfold.
Gfold > 0 || gfold < 0 means it Upregulated or down regulated.

For more information check....
Forum: Bioinformatics 02-20-2014, 12:38 PM
Replies: 5
Views: 1,151
Posted By Krish_143
Thumbs up Hi ccard28, I tried Gfold. This seems good...

Hi ccard28,

I tried Gfold. This seems good when no replicates.. it rank based on logfold data.

For more details
Look at the paper. http://www.ncbi.nlm.nih.gov/pubmed/22923299

Source code...
Forum: Bioinformatics 02-11-2014, 02:10 AM
Replies: 9
Views: 3,026
Posted By Krish_143
RAST annotation. http://rast.nmpdr.org/

RAST annotation.
http://rast.nmpdr.org/
Forum: Bioinformatics 02-11-2014, 02:06 AM
Replies: 5
Views: 1,151
Posted By Krish_143
Hi ccard28, I also work with similar case.....

Hi ccard28,

I also work with similar case.. No replicates but i follow

* Tophat-Cufflinks ( FPKM values from cufflinks not cuffdiff ) or HTSeq read count and then i do analysis based on gene...
Forum: RNA Sequencing 01-22-2014, 05:48 PM
Replies: 1
Views: 1,779
Posted By Krish_143
Any one tried DEAP !...

Any one tried DEAP ! http://sourceforge.net/projects/deapathways/
If you have used any other tools in work please suggest those..
Thanks
Forum: RNA Sequencing 01-22-2014, 08:00 AM
Replies: 1
Views: 1,779
Posted By Krish_143
Differential expression analysis for pathway in bacteria

I have a set of gene list (Kegg ids) and log fold expression values.
I want to identify a pathway that is differentially expressed from samples in case of bacterial genome.
Could any one...
Forum: RNA Sequencing 06-03-2013, 02:40 AM
Replies: 3
Views: 1,145
Posted By Krish_143
Hi, For Identifying ncRNAs, 1) Download...

Hi,

For Identifying ncRNAs,
1) Download directly Rfam database from Rfam.
2) Download Infernal and install it.
using rfam perl script or cmsearch you can find ..

For sRNAs
Use reference...
Forum: RNA Sequencing 06-03-2013, 01:53 AM
Replies: 3
Views: 1,145
Posted By Krish_143
Hi, You can use Rfam for predicting the ncRNAs...

Hi,
You can use Rfam for predicting the ncRNAs and also check SIPHT.
Forum: Bioinformatics 05-31-2013, 07:28 AM
Replies: 3
Views: 2,273
Posted By Krish_143
Hi krobison, when i estimted the genome size...

Hi krobison,

when i estimted the genome size using kmer information (histogram, kmer Peaks)
ESti_Gsize: 2.8mb (at Kmer 31)
Assembled Gsize using SoapDenovo : 5.7mb (Draft)

I will check with...
Forum: Bioinformatics 05-31-2013, 06:03 AM
Replies: 3
Views: 2,273
Posted By Krish_143
Estimating the bacterial genome size using Kmer frequency

Hi,

How to estimate the bacterial genome size (GC rich) when there was no close reference genome ?

At first i tried jellyfish and generated the histogram plots (for all the avail kmers) and...
Forum: RNA Sequencing 03-21-2013, 09:43 AM
Replies: 6
Views: 2,471
Posted By Krish_143
Incase if i do not have replicates, 1) I will...

Incase if i do not have replicates,
1) I will run cufdiff for 2 samples (ctl,sample1)(ctl,sample2)... do it for all and then compare all together.
or
a) I will preffer cufflinks 1st step (all...
Forum: RNA Sequencing 03-21-2013, 01:17 AM
Replies: 3
Views: 2,147
Posted By Krish_143
I am using filterPCRdupl.pl. source: ...

I am using filterPCRdupl.pl.
source:
http://code.google.com/p/condetri/downloads/detail?name=filterPCRdupl.pl
Forum: Bioinformatics 03-19-2013, 06:20 AM
Replies: 5
Views: 3,712
Posted By Krish_143
Acoording to me: cufdiff results will vary...

Acoording to me:
cufdiff results will vary based on how many samples your providing, It always calculate based on the first sample. It will produce better results if one have more no of...
Forum: RNA Sequencing 09-01-2012, 09:58 AM
Replies: 4
Views: 2,686
Posted By Krish_143
Use -G option i.e GTF file for tophat and...

Use -G option i.e GTF file for tophat and cufflinks.
Forum: Bioinformatics 08-27-2012, 04:54 AM
Replies: 4
Views: 2,438
Posted By Krish_143
Hello, Did you found answer !!

Hello,

Did you found answer !!
Forum: RNA Sequencing 08-16-2012, 02:53 AM
Replies: 5
Views: 1,551
Posted By Krish_143
http://code.google.com/p/condetri/ Check...

http://code.google.com/p/condetri/

Check this once..
Quality filtering and PCRduplicate removal :)
Forum: Bioinformatics 07-20-2012, 09:09 AM
Replies: 17
Views: 3,930
Posted By Krish_143
Thanks foxriverlin, _V1.1 Works fine for full...

Thanks foxriverlin, _V1.1 Works fine for full genome.
Forum: Bioinformatics 07-20-2012, 02:41 AM
Replies: 6
Views: 2,150
Posted By Krish_143
Thats fine.. you can ask exactly what genome and...

Thats fine.. you can ask exactly what genome and annotation file they used.. that has to be fixed through out the project so be clear with that.
tc good luck with blast2go. :)
Forum: Bioinformatics 07-20-2012, 02:24 AM
Replies: 6
Views: 2,150
Posted By Krish_143
if you want to identify gene names for Cuff.XXX ...

if you want to identify gene names for Cuff.XXX
i.e 2 ways :

1) you have to run tophat for mapping instead of galaxy and use -G option in tophat and provide ur UCSC annotation file and run...
Forum: RNA Sequencing 07-19-2012, 10:55 PM
Replies: 2
Views: 1,376
Posted By Krish_143
1) Tophat-Cufflinks-CummeRbund. 2) EdgeR

1) Tophat-Cufflinks-CummeRbund.
2) EdgeR
Forum: Bioinformatics 07-19-2012, 10:50 PM
Replies: 6
Views: 2,150
Posted By Krish_143
I do not know about galaxy, but if you use tophat...

I do not know about galaxy, but if you use tophat with -G option (Annotation file)and cufflinks ( annotation file) you will get output with scaffold names.. else it would be like this CUFF.XXXXX....
Forum: Bioinformatics 07-19-2012, 01:35 PM
Replies: 11
Views: 1,723
Posted By Krish_143
simply Tophat is a tool used for mapping the...

simply Tophat is a tool used for mapping the short reads against the genome or transcriptiome. bowtie and bowtie2 are internally used in tophat for old and new versions respectively.

Yeah it was...
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