Forum: Bioinformatics
09-06-2013, 06:03 AM
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Replies: 2
Views: 4,398
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Forum: Bioinformatics
09-06-2013, 04:45 AM
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Replies: 2
Views: 4,398
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 . - . ...
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Forum: Introductions
09-06-2013, 04:34 AM
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Replies: 1
Views: 1,582
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Forum: Bioinformatics
09-02-2013, 03:48 AM
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Replies: 2
Views: 2,807
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Forum: Bioinformatics
07-11-2013, 02:54 AM
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Replies: 1
Views: 1,907
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Forum: Bioinformatics
07-11-2013, 02:13 AM
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Replies: 4
Views: 4,110
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Forum: Bioinformatics
07-11-2013, 02:12 AM
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Replies: 4
Views: 4,110
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Forum: Bioinformatics
07-09-2013, 01:53 AM
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Replies: 4
Views: 4,110
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,...
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Forum: Bioinformatics
07-02-2013, 07:29 AM
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Replies: 3
Views: 2,560
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Forum: Bioinformatics
07-02-2013, 07:23 AM
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Replies: 5
Views: 2,624
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...
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Forum: Bioinformatics
06-26-2013, 11:42 AM
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Replies: 3
Views: 2,560
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...
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Forum: Bioinformatics
06-24-2013, 02:26 AM
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Replies: 1
Views: 2,627
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Forum: Bioinformatics
02-27-2013, 01:43 AM
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Replies: 1
Views: 1,427
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...
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Forum: Bioinformatics
02-26-2013, 03:56 AM
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Replies: 0
Views: 1,476
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,...
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Forum: Bioinformatics
02-15-2013, 05:50 AM
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Replies: 1
Views: 2,647
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
...
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Forum: Bioinformatics
02-15-2013, 05:18 AM
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Replies: 4
Views: 7,171
Query
I am getting the same problem :( . Could you please let me know how you solved this?
Thanks
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Forum: Bioinformatics
02-11-2013, 09:40 AM
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Replies: 2
Views: 4,457
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Forum: Bioinformatics
02-11-2013, 03:16 AM
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Replies: 11
Views: 9,784
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...
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Forum: Bioinformatics
02-05-2013, 07:52 AM
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Replies: 2
Views: 3,284
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Forum: Bioinformatics
02-05-2013, 07:33 AM
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Replies: 2
Views: 3,284
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Forum: RNA Sequencing
02-01-2013, 05:34 AM
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Replies: 3
Views: 2,219
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Forum: RNA Sequencing
02-01-2013, 04:37 AM
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Replies: 3
Views: 2,219
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...
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