[galaxy-user] Question about Extract intron sequences from [gtf file] + [genome FASTA file]

Dear Jen, I am not much of a Galaxy user yet. Some days ago I know something about Galaxy and found it a really wonderful tool. And I am confused by a simple question regarding how to extract intron sequences from [gtf file]; Here is a simple of a gtf file: 1 Cufflinks transcript322

[galaxy-user] How to get random region of 1000-bp window in the chromosome not overlapping specific [gtf] file

Dear Galaxy develop team: As the subject said, I need to obtain random regions which are 1000-bb, and then filter these regions to remove regions overlapping a specific [gtf] file. So can I obtain random regions with Galaxy? I found (Regional Variation)->Make windows may help me, but the tool

Re: [galaxy-user] How to get random region of 1000-bp window in the chromosome not overlapping specific [gtf] file

Hi Jen, Thank you very much! Best, John From: Jennifer Jackson Sent: Friday, August 23, 2013 12:21 AM To: 师云 Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] How to get random region of 1000-bp window in the chromosome not overlapping specific [gtf] file Hello John, Use "

[galaxy-user] Question about expression in Galaxy tools

Hello everyone, I found regular expression could be available in the tool (filter and sort) ->Filter. I wonder whether it could be the same in the tool (Text Manipulation) ->Compute. I have checked that the fuction "len(c4.split('_'))" would return error. So, could anyone tell me if it was pos

Re: [galaxy-user] Question about expression in Galaxy tools

Hi Jen, Thank you for your help. The Galaxy tools can do many things! From: Jennifer Jackson Sent: Friday, August 30, 2013 8:31 AM To: 师云 Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Question about expression in Galaxy tools Hello, There are some tools in the group '

[galaxy-user] How to calculate GC content of transcripts only including exons from a GTF file

Hi everyone, I want to calculate GC content of transcripts in the gtf file like this: chr1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.23955"; transcript_id "CUFF.23955.1"; chr1 Cufflinks exon 3 10 1000 + . gene_id "CUFF.23955"; transcript_id "CUFF.23955.1"; exon_number "1"; chr1 Cufflin

Re: [galaxy-user] How to calculate GC content of transcripts only including exons from a GTF file

hello, jen Thank you for your reply. I though it will return the GC content of each exon. I try it and find that the Galaxy will interpret features. Thank you. John From: Jennifer Jackson Sent: Wednesday, September 18, 2013 6:38 AM To: 师云 Cc: galaxy-user@lists.bx.psu.edu Subject: Re

[galaxy-user] How to filter the sequences containing not[ATCG] character？

Hi Jen,As the title, I have a [fasta] file that obtained from a [gtf] file, >cuff102.1atcgtaaagggcgat>cuff103.1gtcgttgactgtc and I want to get the output like this to filter the sequences that contain any not[ATCG] character? >cuff102.1atcgtaaagggcgat I have a large of sequences to filter.

Re: [galaxy-user] How to filter the sequences containing not[ATCG] character？

d use something like this, with the Select tool and "Matching": ^..*\t[ATCGatcg]+$ (Only one dot is really required, this is just how I always do it. Adds a bit of a format sanity check into the filter). Hope this helps! Jen Galaxy

Re: [galaxy-user] How to filter the sequences containing not[ATCG] character？

urious, I didn't try it that way. There are usually a few ways to do the same thing when using a regex. But, I am glad that this helped a bit and good luck with the query, Jen Galaxy team On 12/9/13 7:06 AM, 朱师云 wrote: Hi,