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Search: Posts Made By: bambus
Forum: Bioinformatics 02-25-2014, 06:03 AM
Replies: 5
Views: 1,279
Posted By bambus
Unhappy Can you please help me how to proceed further to...

Can you please help me how to proceed further to fulfill the steps you mentioned as I am not a very good programmer
Forum: Bioinformatics 02-25-2014, 05:54 AM
Replies: 5
Views: 1,279
Posted By bambus
Does it mean that I have to create a hash of Ids...

Does it mean that I have to create a hash of Ids or?
Forum: Bioinformatics 02-25-2014, 04:06 AM
Replies: 5
Views: 1,279
Posted By bambus
A program to extract the reads and modify the seq ID by adding weight

Hi everyone,

I have a problem in executing the perl script (found online) is given below, a script t0 compare 2 files

1) a file with seq IDs and its weight
2) a file with seq IDs and the...
Forum: Bioinformatics 02-19-2014, 02:30 AM
Replies: 19
Views: 2,929
Posted By bambus
Thank you once again.

Thank you once again.
Forum: Bioinformatics 02-19-2014, 02:25 AM
Replies: 19
Views: 2,929
Posted By bambus
Oh great! its working,thank you very much.

Oh great! its working,thank you very much.
Forum: Bioinformatics 02-19-2014, 02:14 AM
Replies: 19
Views: 2,929
Posted By bambus
Yes,I am sorry forgot to mention , I modified the...

Yes,I am sorry forgot to mention , I modified the data while extracting the columns of interest from original SAM file,but now I executed the script on complete data files.

Again I will try with...
Forum: Bioinformatics 02-19-2014, 01:53 AM
Replies: 19
Views: 2,929
Posted By bambus
yes I did,and I got this following error many...

yes I did,and I got this following error many time with different line numbers


error

Use of uninitialized value in concatenation (.) or string at contig_table.pl line 27, <CTG> line 140568.
Forum: Bioinformatics 02-19-2014, 01:49 AM
Replies: 19
Views: 2,929
Posted By bambus
Input file 2 -list of contigs

Input file 2 -list of contigs
Forum: Bioinformatics 02-19-2014, 01:48 AM
Replies: 19
Views: 2,929
Posted By bambus
input file 1 with mapped reads

input file 1 with mapped reads
Forum: Bioinformatics 02-19-2014, 01:38 AM
Replies: 19
Views: 2,929
Posted By bambus
I am sorry I could attach only 1 file at a time

I am sorry I could attach only 1 file at a time
Forum: Bioinformatics 02-19-2014, 01:21 AM
Replies: 19
Views: 2,929
Posted By bambus
Yes I have an ouput file named 'read_count' with...

Yes I have an ouput file named 'read_count' with "contig ID" Number of Unicals mapped".

Now I also want to print out the "list of Unicals(sequences) that were mapped" "contig sequence" "contig...
Forum: Bioinformatics 02-19-2014, 01:09 AM
Replies: 19
Views: 2,929
Posted By bambus
I am sorry,i am not clear. So now how does...

I am sorry,i am not clear.

So now how does this code works.Do I have to input two files (Mapped sam file to count contig frequency and contig file to extract the sequence)or?
Forum: Bioinformatics 02-19-2014, 12:58 AM
Replies: 19
Views: 2,929
Posted By bambus
Okay,how can I solve this? Can you please...

Okay,how can I solve this?

Can you please help me.
Forum: Bioinformatics 02-18-2014, 11:31 PM
Replies: 19
Views: 2,929
Posted By bambus
Hi Mastal,thank you for the reply. Yes,the...

Hi Mastal,thank you for the reply.

Yes,the lines begin with 'HWI' as you mentioned because I modified the original SAM output file.In general the there are headers in Sam file,but it doesn't harm...
Forum: Bioinformatics 02-18-2014, 08:06 AM
Replies: 19
Views: 2,929
Posted By bambus
Question Metatranscriptomics data analysis:

Hi,

I have a problem with my perl script can anyone please help me out.

I work on Meta transcriptomics data.I assembled my data files(after clustering) using Trinity assembler and also mapped...
Forum: Bioinformatics 01-09-2014, 05:41 AM
Replies: 1
Views: 2,734
Posted By bambus
Hi, I hope you would have got the solution...

Hi,

I hope you would have got the solution for your query,if so can you please share it here as I too got stuck with the same problem.But,the only difference is that I am working with...
Forum: Bioinformatics 12-17-2013, 01:50 AM
Replies: 3
Views: 2,143
Posted By bambus
Thank you for the reply. Do I get better...

Thank you for the reply.

Do I get better scope if I change the assembler before going with mapping step but,not clear which one to use for Meta-transcriptomics data.

Could you suggest me a...
Forum: Bioinformatics 12-10-2013, 02:15 PM
Replies: 3
Views: 2,143
Posted By bambus
Any possible method/tool that could refers the number of overlapping sequences used t

HI,

I work with Metatranscriptomics data(sequenced using Illumina technolgy).I did de-novo transcriptome assembly using SOAP-Denovo-Trans assembler and now looking for a tool/software that could...
Forum: Bioinformatics 11-22-2013, 04:43 AM
Replies: 3
Views: 2,619
Posted By bambus
which denovo assemble to use for assembly of meta-transcriptome data

Hi,

I have couple of questions.

Firstly, I am looking for a denovo assembly tool that can assemble a meta-transcriptome data(paired-end sequence(insert size=300) **consists of mixed sequence...
Forum: Introductions 11-22-2013, 04:35 AM
Replies: 0
Views: 1,515
Posted By bambus
which denovo assemble to use for assembly of meta-transcriptome data

Hi,

I have couple of questions.

Firstly, I am looking for a denovo assembly tool that can assemble a meta-transcriptome data(paired-end sequence(insert size=300) **consists of mixed sequence...
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