SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 22 of 22
Search took 0.00 seconds.
Search: Posts Made By: Shishir
Forum: Bioinformatics 09-06-2013, 06:03 AM
Replies: 2
Views: 4,217
Posted By Shishir
Many thanks! it worked for me.

Many thanks! it worked for me.
Forum: Bioinformatics 09-06-2013, 04:45 AM
Replies: 2
Views: 4,217
Posted By Shishir
parsing the gff file

Hi all,

I have a gff file like:

gn|nvit|C3905550 assmcg CDS 68 646 . - . asmbl_401
gn|nvit|C3905550 assmcg exon 68 646 . - . ...
Forum: Introductions 09-06-2013, 04:34 AM
Replies: 1
Views: 1,564
Posted By Shishir
See the thread here http://www.biostars.org/p/503/

See the thread here http://www.biostars.org/p/503/
Forum: Bioinformatics 09-02-2013, 03:48 AM
Replies: 2
Views: 2,692
Posted By Shishir
Copy the column and paste it with special character

Hi all,

I have a input file like

C3905550 oder CDS 68 646 . - . asmbl_487
C3905550 oder exon 68 646 . - . asmbl_418...
Forum: Bioinformatics 07-11-2013, 02:54 AM
Replies: 1
Views: 1,860
Posted By Shishir
Functional annotation of OrthoMCL groups?

One of the cons of OrthoMCL is "OrthoMCL groups do not have function annotations". Could someone suggest me how to annotate the OrthoMCL groups?
Forum: Bioinformatics 07-11-2013, 02:13 AM
Replies: 4
Views: 4,009
Posted By Shishir
Thanks for the reply!

Thanks for the reply!
Forum: Bioinformatics 07-11-2013, 02:12 AM
Replies: 4
Views: 4,009
Posted By Shishir
Thanks, it seems interesting and I planned to use...

Thanks, it seems interesting and I planned to use it later as currently I am not focused on functional similarity!
Forum: Bioinformatics 07-09-2013, 01:53 AM
Replies: 4
Views: 4,009
Posted By Shishir
Clustering sequences based on sequence similarity

I have 8000 protein sequences that I want to cluster based on similarity (not identity) and select the longest representative sequence from each cluster. I checked several tools like HiFix, SiliX,...
Forum: Bioinformatics 07-02-2013, 07:29 AM
Replies: 3
Views: 2,428
Posted By Shishir
Thanks you all !! :)

Thanks you all !! :)
Forum: Bioinformatics 07-02-2013, 07:23 AM
Replies: 5
Views: 2,574
Posted By Shishir
Relating OrthoMCL clusters with Phylogenetics

I need to relate the OrthoMCL clusters (that I derived from comparison of several insect proteomes) with phylogenetic tree but I am not able to understand how to proceed? I would appreciate your...
Forum: Bioinformatics 06-26-2013, 11:42 AM
Replies: 3
Views: 2,428
Posted By Shishir
Parsing file to retrieve specific pattern

I have a txt file with several rows. Each row contains several words separated by space. I want to print the values which have pattern like amenXXXXXXX (where length of X string is different in many...
Forum: Bioinformatics 06-24-2013, 02:26 AM
Replies: 1
Views: 2,562
Posted By Shishir
Hi, I am facing the same error and still not able...

Hi, I am facing the same error and still not able to solve it. Have you already fixed this error? :confused:
Forum: Bioinformatics 02-27-2013, 01:43 AM
Replies: 1
Views: 1,394
Posted By Shishir
Error in Sam to Bam Conversion

Dear all,

I want to convert Sam file into Bam. I am using command $ samtools view -b -S -o bowtie.glob.bam bowtie.glob.sam
but getting error
Parse error at line 25645: invalid CIGAR character...
Forum: Bioinformatics 02-26-2013, 03:56 AM
Replies: 0
Views: 1,447
Posted By Shishir
Network merging in cytoscape?

Dear all network biologists,

I have two signalling networks that I want to merge with "retaining network layout". I simply merged the networks with network merging utility in cytoscape however,...
Forum: Bioinformatics 02-15-2013, 05:50 AM
Replies: 1
Views: 2,571
Posted By Shishir
need help to solve bowtie2-inspect error

Dear all bowtie users,

I am new in NG-sequencing. I used following command to build index of repeat masked genome by repeatmasker.

bowtie2-build genome_scaffolds.masked.fa my_genome_index
...
Forum: Bioinformatics 02-15-2013, 05:18 AM
Replies: 4
Views: 7,030
Posted By Shishir
Query

I am getting the same problem :( . Could you please let me know how you solved this?

Thanks
Forum: Bioinformatics 02-11-2013, 09:40 AM
Replies: 2
Views: 4,322
Posted By Shishir
Any script to parse HMMsearch results?

I have 146 resulting files of HMMsearch. I used 146 Hmm models to generate these files. Could someone share me any script to parse HmmSearch results?
Forum: Bioinformatics 02-11-2013, 03:16 AM
Replies: 11
Views: 9,451
Posted By Shishir
How to build combined library for repeatmasker?

I want to to perform repeatmasking on ant genome. Ant is also included in the repeat library obtained from Repbase. The library RepeatMaskerLib.embl also contains my species. However, I also...
Forum: Bioinformatics 02-05-2013, 07:52 AM
Replies: 2
Views: 3,228
Posted By Shishir
Thanks Richard!

Thanks Richard!
Forum: Bioinformatics 02-05-2013, 07:33 AM
Replies: 2
Views: 3,228
Posted By Shishir
Any script to format headers in fasta files?

I have a 47GB file to parse. The sequences are in following format:
>TSCS_00041 gene0EA_12345_rframe2_ORF...
Forum: RNA Sequencing 02-01-2013, 05:34 AM
Replies: 3
Views: 2,164
Posted By Shishir
Thanks! I searched for "awk" and realize "sed"...

Thanks!
I searched for "awk" and realize "sed" can do it easily :)
Forum: RNA Sequencing 02-01-2013, 04:37 AM
Replies: 3
Views: 2,164
Posted By Shishir
How to parse FASTQ file?

I am new in NGS. I need to format some fastq files. For example I want to replace characters /1 and /2 with -1 and - 2 in the files having data like @HWUSI-EAS1671_0001:5:1:1022:10290/1.
I tried to...
Showing results 1 to 22 of 22

 


All times are GMT -8. The time now is 03:10 AM.


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