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Search: Posts Made By: seq_newbie
Forum: Bioinformatics 07-20-2011, 09:11 AM
Replies: 3
Views: 2,288
Posted By seq_newbie
Hi Dariober, Thanks for your reply. I'm...

Hi Dariober,

Thanks for your reply. I'm pretty sure the job started running straight away. I'm not sure of the number of reads but I reckon it would be in the millions. I tried uploading log files...
Forum: Bioinformatics 07-20-2011, 05:53 AM
Replies: 3
Views: 2,288
Posted By seq_newbie
Very long tophat run

Hi,

I have submitted a job to the queue on my cluster with 7 successive tophat jobs in the file. It has been 2 days and only the directory for the first job has been created and there is still no...
Forum: Bioinformatics 07-15-2011, 08:25 AM
Replies: 0
Views: 1,243
Posted By seq_newbie
cufflinks query

Hi,

I have used different cufflinks transcripts.gtf files (from different lanes of multiple flow cells) and am using a software that produces splice graphs (gff files) on these files. My output...
Forum: Bioinformatics 07-13-2011, 05:47 AM
Replies: 2
Views: 1,650
Posted By seq_newbie
I'm doing a project on previously sequenced data...

I'm doing a project on previously sequenced data so using tophat and cufflinks. sorry, yes i should have posted this elsewhere. i'll remove it now. thanks
Forum: Bioinformatics 07-13-2011, 01:21 AM
Replies: 2
Views: 1,650
Posted By seq_newbie
Forum: Bioinformatics 07-07-2011, 03:12 AM
Replies: 2
Views: 6,413
Posted By seq_newbie
Convert cufflinks GTF to GFF

Hi,

I am trying to convert a cufflinks GTF file (transcripts.gtf) to a GFF3 file. I have minimal Perl and Python and would not have a clue where to even begin. Someone sent me a python code that...
Forum: Bioinformatics 07-04-2011, 08:37 AM
Replies: 0
Views: 920
Posted By seq_newbie
grepping a GTF file

post deleted
Forum: Bioinformatics 07-04-2011, 07:10 AM
Replies: 0
Views: 1,230
Posted By seq_newbie
GTF format query

Hi,

I want to know is it possible to remove splicing information from a GTF file while retaining gene information? I am using Splicegrapher and I want to get splicing info from my own data and...
Forum: Bioinformatics 06-29-2011, 09:32 AM
Replies: 1
Views: 4,788
Posted By seq_newbie
cufflinks segmentation fault help please

Hi,

I get the output below when I run cufflinks using the command

cufflinks -g /data/shared/genomes/Btau_4.0/Bos_taurus.Btau_4.0.62.gtf --frag-len-mean 201 --frag-len-std-dev 81...
Forum: Bioinformatics 06-23-2011, 08:58 AM
Replies: 1
Views: 6,186
Posted By seq_newbie
How to convert BED format to SAM/BAM?

Hi,

I require a junctions file in SAM format and I have it in BED format. I was wondering is there a tool to convert BED to SAM or BED to BAM? (and I can then use samtools to complete the...
Forum: Bioinformatics 06-21-2011, 07:42 AM
Replies: 1
Views: 1,406
Posted By seq_newbie
Forum: RNA Sequencing 06-14-2011, 07:31 AM
Replies: 1
Views: 1,573
Posted By seq_newbie
Scripture visualisation tool help please

Hi,

I have followed the walkthrough and got a '.bed' and a '.dot' file. However, when I try to view the .bed file with IGV it appears to be showing the entire chromosome rather than the region...
Forum: RNA Sequencing 06-13-2011, 07:39 AM
Replies: 0
Views: 1,417
Posted By seq_newbie
Scripture visualisation tool help please

Hi,

I have followed the walkthrough and got a '.bed' and a '.dot' file. However, when I try to view the .bed file with IGV it appears to be showing the entire chromosome rather than the region...
Forum: RNA Sequencing 06-09-2011, 08:02 AM
Replies: 0
Views: 1,826
Posted By seq_newbie
GenomeGraphs (bioconductor) query

Hi,

I want to know is GenomeGraphs, a Bioconductor package, suitable for visualising all alternative splicing events (e.g. mutually exclusive, alternate 3', exon skipping etc). Also, If you could...
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