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Search: Posts Made By: kurban910
Forum: Bioinformatics 01-02-2016, 03:25 AM
Replies: 7
Views: 2,894
Posted By kurban910
thanks @sgoetz yeah, blast2go sure is a fine...

thanks @sgoetz
yeah, blast2go sure is a fine tool. finished the job already.
Forum: Bioinformatics 12-01-2015, 07:30 PM
Replies: 3
Views: 1,002
Posted By kurban910
thanks you @mastal.

thanks you @mastal.
Forum: Bioinformatics 12-01-2015, 01:39 PM
Replies: 3
Views: 1,002
Posted By kurban910
about uniprot sprot.fasta header

hey guys,
i wanna ask a question about uniprot fasta file header.

in the header shown as below:

[email protected]:~/Desktop/Uniprot$ zcat uniprot_sprot.fasta.gz | more...
Forum: Bioinformatics 11-30-2015, 12:54 AM
Replies: 7
Views: 2,894
Posted By kurban910
hi @frankM and @Dampor did you use Annocript...

hi @frankM and @Dampor
did you use Annocript for the annotaion of your transcriptome or some other tools? when you were doing annotaion did you use a server or just a PC would be fine? because i...
Forum: General 08-03-2015, 01:13 AM
Replies: 16
Views: 9,296
Posted By kurban910
hi @cacti and @Richard Finney what i have is...

hi @cacti and @Richard Finney
what i have is only multiple transcript sequences (which came from RNA-seq assembly), so i used "blast2go" software blasted them with ncbi nr, then interpro scan (which...
Forum: General 07-20-2015, 10:50 PM
Replies: 16
Views: 9,296
Posted By kurban910
hello to all and @WhatsOEver, the sample i have...

hello to all and @WhatsOEver,
the sample i have been working with also a non model species. after finding differential expressed unigene in its transcriptome data i have used Blast2GO done exactly...
Forum: Bioinformatics 07-03-2015, 09:30 AM
Replies: 2
Views: 1,037
Posted By kurban910
Unhappy thanks @Richard, the commend really works like...

thanks @Richard,
the commend really works like a charm, but the total sequences i wanna extract are 519, so how could i change my file formation
100141790
100142111
100142176
100142203...
Forum: Bioinformatics 07-03-2015, 06:21 AM
Replies: 2
Views: 1,037
Posted By kurban910
Get Protein Sequences fasta file by using Entrez Gene Ids

I want to get a protein sequences FASTA file for a given list of Entrez Gene IDs, which is shown as blow:

[email protected]:~/Desktop$ more Triboliumcastaneum_tf_id.txt
100141790
100142111...
Forum: Bioinformatics 06-21-2015, 02:06 AM
Replies: 14
Views: 5,584
Posted By kurban910
thanks @Zapages and @Chipper , i will check both...

thanks @Zapages and @Chipper , i will check both of them.
Forum: Bioinformatics 06-20-2015, 03:39 AM
Replies: 14
Views: 5,584
Posted By kurban910
how to draw venn diagram

Dear all,
what i am about to ask is one insanely easy question, but i need an instruction.
some people draw venn diagram for the results of their transcriptome blast against different database;...
Forum: Bioinformatics 06-18-2015, 09:44 AM
Replies: 11
Views: 2,894
Posted By kurban910
hey @dpryan, it seems like i did not make...

hey @dpryan,
it seems like i did not make myself clear, sorry about it.
i used edgeR got this:

et <- exactTest(y, dispersion=bcv^2)
> summary(de <- decideTestsDGE(et))
[,1]
-1 273
0 ...
Forum: Bioinformatics 06-15-2015, 11:19 AM
Replies: 11
Views: 2,894
Posted By kurban910
hi @Devon, i have finished differential the...

hi @Devon,
i have finished differential the expression analysis with edgeR with the help of its user guide, then searched some stuff about how to export data from R. but i still do not know how to...
Forum: Bioinformatics 06-13-2015, 06:07 AM
Replies: 11
Views: 2,894
Posted By kurban910
thank you @Devon Ryan, really:)

thank you @Devon Ryan, really:)
Forum: Bioinformatics 06-13-2015, 05:59 AM
Replies: 11
Views: 2,894
Posted By kurban910
hi @dpryan, thanks for the reply. but what do u...

hi @dpryan,
thanks for the reply. but what do u mean by "index the results"? do u mean index the sam file i got after aligning the reads to trinity.fasta by using bowtie2?

does that mean i...
Forum: Bioinformatics 06-13-2015, 04:51 AM
Replies: 11
Views: 2,894
Posted By kurban910
i wanna repeat the same question, because i am...

i wanna repeat the same question, because i am working with the transcripome data of non model organism, but during downstream analysis i am often required GFT files of the fasta file i work with,...
Forum: RNA Sequencing 06-12-2015, 08:54 PM
Replies: 2
Views: 2,755
Posted By kurban910
hello @alan_sm you said you made GTF file for...

hello @alan_sm
you said you made GTF file for the assembled transcripts FASTA file with a Perl script. could you please share the script?
once i really needed to make GTF file myself but could...
Forum: RNA Sequencing 06-09-2015, 04:44 AM
Replies: 9
Views: 1,728
Posted By kurban910
Hi @dpryan yes , i am starting with...

Hi @dpryan


yes , i am starting with fasta file. i have no problem with reads alignment and mapped reads counting, but R is new to me . today i have read the edgeR user guide and still did not...
Forum: RNA Sequencing 06-09-2015, 04:13 AM
Replies: 9
Views: 1,728
Posted By kurban910
not yet, i just assembled the reads got the...

not yet, i just assembled the reads got the trinity.fasta file.
Forum: RNA Sequencing 06-09-2015, 03:46 AM
Replies: 9
Views: 1,728
Posted By kurban910
thanks @GenoMax:) my following questions...

thanks @GenoMax:)

my following questions might be ridiculously easy, but there is no one in my lad to give some tips about these analysis. so i am going to ask them here anyway, please bear with...
Forum: RNA Sequencing 06-09-2015, 02:16 AM
Replies: 9
Views: 1,728
Posted By kurban910
hey guys, i have never used edgeR, DESeq, and...

hey guys,
i have never used edgeR, DESeq, and baySeq packages before, but now i need to use them analyze my RAN-seq data. my question is can i run these packages on my laptop to analysis...
Forum: De novo discovery 06-05-2015, 11:44 AM
Replies: 0
Views: 1,442
Posted By kurban910
i got two different trinity.fasta by using two version of trinity

hi guys,
we have RNA-seq data sequenced of an insect in 2012, and assembled them by using one of the Trinity 2011 versions at the time (got the trinity.fasta) . now i analyzed the sequence length...
Forum: Introductions 06-04-2015, 07:34 PM
Replies: 11
Views: 2,159
Posted By kurban910
hey @arcolombo698, i sued samtools got the fai...

hey @arcolombo698,
i sued samtools got the fai file. and when i tried to do the length distribution by R i changed my gene.fa.fai file to gene.txt. then i used this commend as its mentioned...
Forum: Introductions 06-04-2015, 07:22 PM
Replies: 11
Views: 2,159
Posted By kurban910
hi @arcolombo698, could you be little bit more...

hi @arcolombo698,
could you be little bit more specific?!
how could i do what i want by using FastQC when my input file is fasta?
Forum: Introductions 06-04-2015, 07:14 PM
Replies: 11
Views: 2,159
Posted By kurban910
yeah , that will work. thanks @Brian Bushnell

yeah , that will work. thanks @Brian Bushnell
Forum: Introductions 06-04-2015, 09:43 AM
Replies: 11
Views: 2,159
Posted By kurban910
hi @antoza, did you find way to solve your...

hi @antoza,
did you find way to solve your problem? if u did could you share your experience?
i am facing with the same task right now.
thanks.
Showing results 1 to 25 of 58

 


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