SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 51
Search took 0.00 seconds.
Search: Posts Made By: chayan
Forum: Bioinformatics 05-09-2019, 04:54 PM
Replies: 1
Views: 546
Posted By chayan
bash loop to count multiple words from multiple corresponding files

I have generated multiple read mapping files (.sam) generated with bowtie2 "--no-unal" parameter. As the number of files are huge (7 reference genomes mapped against >6000 reads) i want a loop to...
Forum: Bioinformatics 05-01-2019, 08:05 AM
Replies: 8
Views: 910
Posted By chayan
I don't have installation access and I just ask...

I don't have installation access and I just ask them but they will take month to respond I know. In the meanwhile I am trying to bypass it using Anaconda. Do let me know if there is any better ways...
Forum: Bioinformatics 05-01-2019, 07:12 AM
Replies: 8
Views: 910
Posted By chayan
Hi I am running parallel jobs but all the...

Hi

I am running parallel jobs but all the getting the following error which I am not sure from my array script or something else.

Slurm Array

#!/bin/bash

#SBATCH --job-name=Bowtie_Array #...
Forum: Bioinformatics 04-24-2019, 10:58 AM
Replies: 8
Views: 910
Posted By chayan
Thanks for your prompt response. If I...

Thanks for your prompt response.

If I understood correctly I have to submit >6500 slurm array? Well this particular server has 56 nodes and each with 40 threads. Every single job is taking more...
Forum: Bioinformatics 04-24-2019, 10:20 AM
Replies: 8
Views: 910
Posted By chayan
Multiple fastq alignment with bowtie2 in server

Hi!
I'm trying to map multiple sra files (>6500) with bowtie2 against my reference genome. I am running slurm script in a server. While mapping for single sequence is working fine but when running...
Forum: Ion Torrent 09-08-2017, 07:47 PM
Replies: 0
Views: 2,324
Posted By chayan
Uniprot IDs for a whole genome

Hallo,

I have extracted a population bin from a metagenome. I have also uploaded the same to the genebank. But according to their rule NCBI won't include it in the refseq as it has came from a...
Forum: Bioinformatics 12-18-2015, 11:24 AM
Replies: 6
Views: 1,884
Posted By chayan
as i am not sure that my reply to your message...

as i am not sure that my reply to your message has been sent properly or not (due to network failure) thats why i am pasting it here also...

from the metagenomic bin i have extracted the 16s rRNA...
Forum: Bioinformatics 12-18-2015, 10:57 AM
Replies: 6
Views: 1,884
Posted By chayan
that will be awesome...you want me to send the...

that will be awesome...you want me to send the gbk file along with the list of genes that i want to extract from the gbk??? then please give me ur mail id...i can send you the gbk files or the NCBI...
Forum: Bioinformatics 12-14-2015, 05:57 PM
Replies: 6
Views: 1,884
Posted By chayan
Hii every one..can any one help me with this...

Hii every one..can any one help me with this problem???
Forum: Bioinformatics 12-14-2015, 06:00 AM
Replies: 6
Views: 1,884
Posted By chayan
Exclamation Extract Sequence From The Genome?

Hi,

I have extracted a population genome bins from a metagenome..now i want to give a taxonomic position to that bin..for that matter multiple sequence based tree will be helpful..can any one...
Forum: Bioinformatics 10-14-2015, 11:13 AM
Replies: 3
Views: 1,683
Posted By chayan
No not at all rubbishing..sorry if I...

No not at all rubbishing..sorry if I misunderstood...i just said as i am not a bioinformatician so i found it tough to use..anyway thanks for your suggestion
Forum: Bioinformatics 10-14-2015, 01:40 AM
Replies: 3
Views: 1,683
Posted By chayan
Unhappy PCA plots based on nucleotide word frequency (k-mer) of assembled contigs &/or raw re

Which utility package (preferable web-based) is available to generate PCA plots based on nucleotide word frequency (k-mer) of assembled contigs &/or raw reads ??? I found R bit tricky and tough to...
Forum: Bioinformatics 01-04-2015, 11:10 PM
Replies: 4
Views: 1,680
Posted By chayan
And if possible basicslly i want to extract only...

And if possible basicslly i want to extract only the integer "517" after the "size=" portion

thnks
Forum: Bioinformatics 01-04-2015, 10:51 PM
Replies: 4
Views: 1,680
Posted By chayan
Extraction of a portion of a fasta header

Hi,

I have a multi fasta file whose header is like below,

">WLPTB:00031:00193;size=517;"

now i want to extract just the "size=517" portion from all the sequences..

any help???
Forum: Bioinformatics 09-05-2014, 11:10 AM
Replies: 2
Views: 1,161
Posted By chayan
Yes they have responded to my request..thanks for...

Yes they have responded to my request..thanks for your reply
Forum: Bioinformatics 09-04-2014, 11:14 PM
Replies: 2
Views: 1,161
Posted By chayan
Editing genome assemblies with Cytoscape

Hi All,

I have performed a metagenomic assembly from Ion-Proton reads. Now I want to check my assembly using Cytoscape for probable misassembles. I found a very usefull guide in the folowing link...
Forum: Ion Torrent 08-26-2014, 12:42 PM
Replies: 12
Views: 8,699
Posted By chayan
Okk i understand..but i want a different...

Okk i understand..but i want a different utility..i have a metagenomic read files..it is more likely that within that file reads coming from a particular organism will have a similar kind of k-mer...
Forum: Ion Torrent 08-26-2014, 01:12 AM
Replies: 12
Views: 8,699
Posted By chayan
Okk thanks to both of you, additionally is there...

Okk thanks to both of you, additionally is there a tool or utility which allow k-mer based read extraction?
Forum: Bioinformatics 06-19-2014, 11:31 PM
Replies: 2
Views: 2,075
Posted By chayan
Thanks i did it already but additionaly i want to...

Thanks i did it already but additionaly i want to cluster my samples based on the frequency of cog categories and finaly plot in NMDS (nonmetris mds), as i am not well aware of this so now i am...
Forum: Bioinformatics 06-10-2014, 10:23 PM
Replies: 2
Views: 2,075
Posted By chayan
Clustering of samples based on tetra nucleotide frequency

Hi All,

I have assembled several metagenomic samples of various sequencing depth. The contigs have been annotated with COG. Now I want to cluster them based on tetra nucleotide frequency and COG...
Forum: Bioinformatics 05-09-2014, 12:58 PM
Replies: 4
Views: 1,269
Posted By chayan
thanks.. but i have never used R also... what i...

thanks.. but i have never used R also... what i understand from the Mclust manual, if my matrix is like this

A B C D E
i 20 30 15 43 87
ii 12 54 3 76 56
iii 45 78 4 99 54

i should...
Forum: Bioinformatics 05-09-2014, 12:44 PM
Replies: 4
Views: 1,269
Posted By chayan
thanks to both of you. As i am going through both...

thanks to both of you. As i am going through both the manuals, it will take some time as i am a hardcore biology guy, i want to clear one my query.. my matrix structure is like this
A B ...
Forum: Bioinformatics 05-09-2014, 12:29 PM
Replies: 2
Views: 2,100
Posted By chayan
Best Assembler for Metagenome Assembly

Hii All,

I have couple of questions regarding metagenomic assembly..

1. What is the best assembler (open source please!!) for a denovo or reference based assembly for iontorrent/proton reads??...
Forum: Bioinformatics 05-07-2014, 07:28 AM
Replies: 4
Views: 1,269
Posted By chayan
Clustering a two-D matrix

Hii All,

I have generated a 2-D matrix based on NGS data which has cog scores in one axis (Y-axis) and sample no in other axis. Now i want to cluster this matrix based on the cog scores to find...
Forum: Bioinformatics 04-27-2014, 10:17 PM
Replies: 2
Views: 1,368
Posted By chayan
counting the details of a .SFF file

Hii All,

Is there a way/utility to get the details of any .SFF file?? I want to
calculate the total no of reads, bases, and Q20 bases in my Ion .SFF file.
I mean utilities which are there for...
Showing results 1 to 25 of 51

 


All times are GMT -8. The time now is 01:32 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO