Re: [galaxy-user] galaxy-user Digest, Vol 74, Issue 15 - galaxy-user

16 Aug 2012

      Thanks Ariel.
Bony
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Subject: galaxy-user Digest, Vol 74, Issue 15
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Today's Topics:
1. Re: Lift Over bam files (Jennifer Jackson)
   2. Linking to Compressed Data (Branden Timm)
   3. Re: How to decide "Mean Inner Distance between Mate Pairs"?
      (Jennifer Jackson)
   4. Can I convert paired-end datasets into single end ones?
      (Du, Jianguang)
   5. Re: Can I convert paired-end datasets into single end ones?
      (Jennifer Jackson)
   6. Re: Galaxy toolshed-vcftools (Jennifer Jackson)
   7. Do I need to allow indel search? (Du, Jianguang)
   8. Use Own Junctions or not (Du, Jianguang)
   9. Re: copy number variation detcetion in Glaxay (Jennifer Jackson)
  10. Cuffdiff errors (Yan He)
  11. Re: Cuffdiff errors (Jennifer Jackson)
  12. Re: copy number variation detcetion in Glaxay (Mathew Bunj)
  13. Re: Do I need to allow indel search? (Jennifer Jackson)
----------------------------------------------------------------------
Message: 1
Date: Wed, 15 Aug 2012 09:05:41 -0700
From: Jennifer Jackson jen@bx.psu.edu
To: Geert Vandeweyer geertvandeweyer@gmail.com
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Lift Over bam files
Message-ID: 502BC8D5.8020804@bx.psu.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hello Geert,
For the best results, especially for SNPs, you will want to map directly to the target genome. The genome Galaxy is using is the same primary human genome the GATK team also uses - the 1000 genomes build 37 -> "hg_g1k_v37". Click on the GATK links from one of the tools to see the details. GATK provides liftOver files between the the genomes, and you could install and use these with the liftOver tool, but not for BAM datasets. Inputs are BED, Interval, GFF. (BAM -> SAM -> interval).
GATK also provides indexes (lifted) for hg19, but Galaxy does not provide an hg19 genome that is sorted appropriately for GATK, or at least not yet. RNA-seq tools and most other tools up until now required sorting in one way, and now GATK requires sorting in another, but keeping the database dbkey the same is important for visualization and other functions. It can get complicated when moving between tools in a history. We will likely have some 'best practice' solutions soon, but for now, use the 1000 genomes build to keep it all simple:
Human (Homo sapients) (b37): hg_g1k_v37
The good news is that installing this genome has been greatly simplified. The genome and indexes are now available on an rsync server.
You can simply download and add the genome directory and all the contents. You will still need to create the .loc file entries but the rest is done.
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
The "dbkey" is "hg_g1k_v37"
Hopefully one of the options works out for you!
Jen
Galaxy team
ps: You post ended up threading behind another post. I am not sure if this was because you started with a reply, but changed the subject line?
This is not enough to start a new thread. Instead, please create a brand new message in your email client, then copy over the mailing list email address, add a subject line, and this will start a new thread that will get tracked and not missed. Thanks!
On 8/15/12 1:16 AM, Geert Vandeweyer wrote:
...
Hi all,
We have recieved some bam files that were aligned to hg18. What would
be the easiest workflow to get a VCF file from GATK in build hg19 ? We
are running a local galaxy with only hg19 for the moment. Lifting the
bam file would be my first choice, providing support to hg18 by
generating all indices would be my last :-)
Best regards,
Geert

The Galaxy User list should be used for the discussion of Galaxy
analysis and other features on the public server at usegalaxy.org.
Please keep all replies on the list by using "reply all" in your mail
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--
Jennifer Jackson
http://galaxyproject.org
------------------------------
Message: 2
Date: Wed, 15 Aug 2012 11:09:37 -0500
From: Branden Timm btimm@wisc.edu
To: galaxy-user@lists.bx.psu.edu
Subject: [galaxy-user] Linking to Compressed Data
Message-ID: 502BC9C1.8090903@wisc.edu
Content-Type: text/plain; CHARSET=US-ASCII; format=flowed
Hi All,
   Is it possible to link to compressed files in a Galaxy data library?
We receive all of our NGS data in bz2 or gzip format for obvious
reasons, just wondering if I have to decompress it on the filesystem
before I link to it or not.  Thanks!
--
Branden Timm
btimm@glbrc.wisc.edu
------------------------------
Message: 3
Date: Wed, 15 Aug 2012 09:27:36 -0700
From: Jennifer Jackson jen@bx.psu.edu
To: Sean Davis sdavis2@mail.nih.gov, "Du, Jianguang"
        jiandu@iupui.edu
Cc: "galaxy-user@lists.bx.psu.edu" galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] How to decide "Mean Inner Distance between
        Mate Pairs"?
Message-ID: 502BCDF8.4030005@bx.psu.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Great advice Sean!
Jianguang, this is the correct analysis - mapping the data to test the
actual insert size of the library as sequenced. The experimental notes
at SRA are just a starting place, the data is truth. A sample through
TopHat itself might produce more precise results. I suspect the coverage
on your top Blastn HSP is not complete, breaking off where it hits a
splice. And that you have some bias for sequences/hits that cross
junctions near ends. But overall, none of this would likely make that
much of a difference in the analysis as a whole.
Good luck!
Jen
Galaxy team
On 8/15/12 8:39 AM, Sean Davis wrote:
...
On Wed, Aug 15, 2012 at 11:13 AM, Du, Jianguang <jiandu@iupui.edu
mailto:jiandu@iupui.edu> wrote:
Dear All,

I am analyzing the downloaded RNA-seq datasets. However I am not
sure how much is Mean Inner Distance between Mate Pairs for these
paired-end datasets.

Take a paired-end RNA-seq dataset as an example, there is a
description for this dataset in SRA database of NCBI: "Layout:
PAIRED/, Orientation: /5'-3'-3'-5'/, Nominal length: /400/, Nominal
Std Dev: /20"

At first I thought the Mean Inner Distance between Mate Pairs should
be 325bps because the length of reads on both ends is 36bps. However
when I aligned the sequence of the paired reads on to transcripts
and genome using BLASTn, the distance between the paired reads
is about 200bps. How should I decide the Mean Inner Distance between
Mate Pairs in my case?

The information from SRA is likely only an approximation.  SRA does not
validate these details, I do not think.
You can probably use the distribution from your data as the best estimate.
Sean
Thanks.

Jianguang Du

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at usegalaxy.org.  Please keep all replies on the list by
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--
Jennifer Jackson
http://galaxyproject.org
------------------------------
Message: 4
Date: Wed, 15 Aug 2012 16:59:27 +0000
From: "Du, Jianguang" jiandu@iupui.edu
To: "galaxy-user@lists.bx.psu.edu" galaxy-user@lists.bx.psu.edu
Subject: [galaxy-user] Can I convert paired-end datasets into single
        end     ones?
Message-ID:
        2B3C356FD95D6A41B0CCFF77102E5EDF12867830@IU-MSSG-MBX106.ads.iu.edu
Content-Type: text/plain; charset="iso-8859-1"
Dear All,
I have some paired-end datasets to be analyzed, but I am not sure about their Mean Inner Distance between Mate Pairs.
Can I convert these paired-end datasets into single-end ones and use them as single-end dataset as follows?
1) Use the tool "Manipulate FASTQ" to convert the sequence of reverse reads into its reverse-complement counter part, so that all of the reverse reads actually become forward reads.
2) run Tophat on the manipulated datasets as single-end ones.
Thanks.
Jianguang