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Forum: Bioinformatics 10-13-2015, 06:02 AM
Replies: 5
Views: 2,885
Posted By wanfahmi
Hi areyes, can this script applied to the current...

Hi areyes, can this script applied to the current DEXSeq version? How can I get the real exon? Thanks
Forum: Bioinformatics 09-02-2015, 11:36 PM
Replies: 9
Views: 5,285
Posted By wanfahmi
Can DEXSeq handle more than 70 samples to...

Can DEXSeq handle more than 70 samples to analyse? I have different human tissue to analyse which not same as normal vs disease as shown in vignette.
Forum: Bioinformatics 08-24-2015, 04:04 AM
Replies: 10
Views: 6,067
Posted By wanfahmi
Hello I faced similar problem but how to...

Hello

I faced similar problem but how to solve the problem anyway?

I just ran cuffdiff across 30 human tissues to detect differentially expressed across tissues. The file output from...
Forum: Bioinformatics 06-10-2015, 03:26 AM
Replies: 33
Views: 10,566
Posted By wanfahmi
The problem was the output file is a binary file....

The problem was the output file is a binary file. There was no command to specify the output. I tried the webserver as you suggest but end up no result page after they finished processing my GTF...
Forum: Bioinformatics 06-09-2015, 02:30 PM
Replies: 33
Views: 10,566
Posted By wanfahmi
I got 100 samples to analyse so it would be...

I got 100 samples to analyse so it would be useful and efficient if I can run it on server. I can process using the command line but the output of astalavista was in binary which I can't open it....
Forum: Bioinformatics 06-09-2015, 05:13 AM
Replies: 33
Views: 10,566
Posted By wanfahmi
How do you get the output from AStalavista? I am...

How do you get the output from AStalavista? I am using the commandline provide in the help section but it doesn't help. The command I used was

./astalavista -t asta -i transcript.gtf -o output.txt...
Forum: Bioinformatics 04-23-2015, 04:33 AM
Replies: 38
Views: 26,028
Posted By wanfahmi
Can we get the FPKM value only without through a...

Can we get the FPKM value only without through a long process of Cuffdiff? I do have 100 samples and each sample has 3 biological replicates. I am only interested in FPKM value which will later use...
Forum: Bioinformatics 02-27-2015, 04:51 AM
Replies: 46
Views: 27,677
Posted By wanfahmi
How can I get a read count per exon per...

How can I get a read count per exon per transcript in a particular gene from BAM file? I tried using htseq-count with id_attr=transcipt_id but this approach does not give me the read count per exon...
Forum: RNA Sequencing 05-27-2013, 05:10 AM
Replies: 15
Views: 9,236
Posted By wanfahmi
Hi sagarc88 Which one Tophat or Tophat2 does...

Hi sagarc88

Which one Tophat or Tophat2 does have the ability multimapper as you mention? I tried using the samtools -F 256, it gave me 0. Does it mean my bam file doesn't have multimapped reads?
Forum: Bioinformatics 04-16-2013, 03:30 PM
Replies: 7
Views: 4,732
Posted By wanfahmi
Hi Simon, Sorry for the silly question....

Hi Simon,

Sorry for the silly question. Alright let straight forward. I got 2 raw data from two different platform (microarray and rna-seq). As we all know that RNA-seq data perform better than...
Forum: Bioinformatics 04-16-2013, 06:59 AM
Replies: 7
Views: 4,732
Posted By wanfahmi
Hi Simon, Already got the raw data count...

Hi Simon,

Already got the raw data count from RNA-seq which I used htseq-count. But, how to make a scatter plot to compare both RNA-seq and microarray data? Thank you
Forum: Bioinformatics 02-01-2013, 02:31 AM
Replies: 38
Views: 25,551
Posted By wanfahmi
Hey Everybody, The reason why the tophat...

Hey Everybody,

The reason why the tophat couldn't find the bowtie indexes because you didn't specify the path in your working directory.

The easiest way you just make link to your working...
Forum: Introductions 01-16-2013, 05:28 AM
Replies: 13
Views: 11,514
Posted By wanfahmi
It's work! Tq simon..

It's work! Tq simon..
Forum: Introductions 01-16-2013, 12:59 AM
Replies: 13
Views: 11,514
Posted By wanfahmi
Hi Simon, I took the gtf file from ENSEMBL...

Hi Simon,

I took the gtf file from ENSEMBL (genes.gtf). Here is the file looks like. It is possible to change from identifier to gene name? Thank you.
Forum: Introductions 01-15-2013, 06:26 AM
Replies: 13
Views: 11,514
Posted By wanfahmi
Hi, How can we change the identifier to real...

Hi,

How can we change the identifier to real gene name. The gene name should be taken from genes.gtf, isn't it? Thank you
Forum: Bioinformatics 01-14-2013, 06:17 AM
Replies: 24
Views: 15,167
Posted By wanfahmi
How can I convert the ENSG00000261838 to real...

How can I convert the ENSG00000261838 to real name of genes? Or is there any parameter do I need to use prior using htseq-count? Thank you
Forum: Bioinformatics 01-11-2013, 01:48 AM
Replies: 41
Views: 15,806
Posted By wanfahmi
Sorry to add up, I was using GTF file from...

Sorry to add up,

I was using GTF file from ensembl (genes.gtf), thus the "ENSG00000261838" is a gene from human. How could I replace the number to name of gene? What should I do? Thanks
Forum: Bioinformatics 01-10-2013, 08:05 AM
Replies: 41
Views: 15,806
Posted By wanfahmi
Hi Simon, Already sort according to name and...

Hi Simon,

Already sort according to name and run htseq-count and here is the output;

ENSG00000261838 0
ENSG00000261839 2
ENSG00000261840 6
ENSG00000261841 0
ENSG00000261842 0
no_feature ...
Forum: Bioinformatics 01-10-2013, 03:05 AM
Replies: 41
Views: 15,806
Posted By wanfahmi
Hi Simon, How could I sorted the SAM...

Hi Simon,



How could I sorted the SAM file according to name? Thank you
Forum: Introductions 12-20-2012, 04:34 AM
Replies: 13
Views: 11,514
Posted By wanfahmi
HI Hanshart, Is there any problem with my...

HI Hanshart,

Is there any problem with my sort? It showed segmentation fault but this accepeted_hits.bam is from tophat output. Thanks
Forum: Introductions 12-20-2012, 03:51 AM
Replies: 13
Views: 11,514
Posted By wanfahmi
Hi Dario, I am trying to do exactly you...

Hi Dario,

I am trying to do exactly you mention above, the first step is to sort the accepted_hits.bam. But it looks like to generate a lots of file. Does it looks correct? As attached. Thanks.
Forum: Bioinformatics 12-17-2012, 05:16 AM
Replies: 34
Views: 12,779
Posted By wanfahmi
Problem solved! The download file at the...

Problem solved!

The download file at the webpage isn't working. I downloaded again from the "Version History" 1.1.0, is working. Maybe the admin didn't realize it.
Forum: Bioinformatics 12-17-2012, 04:33 AM
Replies: 34
Views: 12,779
Posted By wanfahmi
Hi, I just downloaded the bam2fastq file but...

Hi,

I just downloaded the bam2fastq file but I cannot extract it. Is there any problem with the file? Thanks

--

tar -xzf bam2fastq-1.1.0.tgz

gzip: stdin: unexpected end of file
tar:...
Forum: Bioinformatics 12-14-2012, 02:33 AM
Replies: 7
Views: 17,968
Posted By wanfahmi
Hi, How could we extract reads for specific...

Hi,

How could we extract reads for specific locus / gene from accepted_hits.bam file? Is that possible? Could we get the fastq / fasta from it? Thank you
Forum: Bioinformatics 12-03-2012, 07:05 AM
Replies: 23
Views: 14,696
Posted By wanfahmi
Problems solved! thank you. I did create a...

Problems solved! thank you.

I did create a file that only contains the names not the contains of file. Its running.
Showing results 1 to 25 of 34

 


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