SEQanswers

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-   -   Software packages for next gen sequence analysis (http://seqanswers.com/forums/showthread.php?t=43)

apfejes 10-09-2009 12:18 PM

Hi Ka123$,

I emailed it to you last week. If it didn't arrive, it may be that it was too large. Can you check on the maximum email attachment size your email can accept? The attachment was 10.6Mb, which may have been to large.

If that's the case, please let me know, and I'll arrange to host it somewhere for you.

Anthony

eslondon 10-17-2009 02:43 AM

Same log problem, probably silly but still...
 
When using Separatereads.jar I have no issues if I use only 1 input file, all works fine. If I try to use it in the way described in the example, i.e. using the asterisk to provide it as input several input files in one directory, it decides that it should try to write the output into one of the inputs...

Here is the command line:
java -jar ~/programs/VancouverShortRead/fp4/SeparateReads.jar bowtie /data/bioinfo/302KC/*.map /data/bioinfo/Analysis/mapping/brain/

And here it the output:
Error: Coundn't create log file : /data/bioinfo/302KC/HCT449_brain_s_2_sequence.fastq.map/SeparateReads.log

Any tips?

thanks

Elia

eslondon 10-17-2009 02:47 AM

Hmmm... must be something silly that I will regret having posted... I have the same problem with SortFiles as well... rather than taking in all *.gz, it takes the first one, and assumes the second one is the location for the log file.... could it be a shell/environment issue?

Update: fails also without using asterisk... basically it allows only one input file, and takes the 2nd input file as the output directory

Elia

apfejes 10-17-2009 01:57 PM

Hi Elia,

The short answer is that you don't need to run separateReads/SortReads on map files, as the reads they contain are already sorted by chromosome and start position. Of course, if you're trying to do something other than run FindPeaks with them, that's a different story.

Edit: I should probably also add that it's not a good idea to try. These two particular utilities were intended only for use with text format files - not pre-sorted binary files. I've never tested it out on a .map file.

Anthony

greggrant 10-27-2009 05:12 AM

Thanks for this list, that's really awesome. What do people think is the best way at this point to map approximately 5 million 100 bp reads to a transcriptome? I'm looking for alignment allowing (a specified number of) mismatches but no gaps. Thanks again for this list!

dan 10-27-2009 06:28 AM

Quote:

Originally Posted by greggrant (Post 9769)
Thanks for this list, that's really awesome. What do people think is the best way at this point to map approximately 5 million 100 bp reads to a transcriptome? I'm looking for alignment allowing (a specified number of) mismatches but no gaps. Thanks again for this list!

I'd map against the genome (you never know) using bowtie or SOAP.

You can look them up here:

http://seqanswers.com/wiki/Software

greggrant 10-27-2009 07:22 AM

Quote:

Originally Posted by dan (Post 9775)
I'd map against the genome (you never know) using bowtie or SOAP.

You can look them up here:

http://seqanswers.com/wiki/Software

Those options won't find things that map across exon/exon junctions. I need something that can map ungapped to the transcriptome, probably BLAST will do the trick, bu there should be something faster.

apfejes 10-27-2009 08:11 AM

We use a database of all predicted/potential exon/exon junctions in addition to the genome, and then use maq/bwa - it seems to do very well.

ewilbanks 10-27-2009 10:33 AM

Try TopHat http://tophat.cbcb.umd.edu/

It uses Bowtie to map reads and analyzes the mapping results to identify splice junctions between exons.

Xi Wang 10-30-2009 01:39 AM

Hi all,

Have you noticed a review on ChIP-seq and RNA-seq computational studies? It mentioned and summarized some available tools on ChIP-seq and RNA-seq data processing.

http://www.nature.com/nmeth/journal/...meth.1371.html

Review
Nature Methods 6, S22 - S32 (2009)
doi:10.1038/nmeth.1371
Computation for ChIP-seq and RNA-seq studies
Shirley Pepke1, Barbara Wold2 & Ali Mortazavi2


Best wishes,
Xi

wuhoucdc 11-05-2009 09:32 PM

Thanks Sci_guy pasted such a great resource!

sci_guy 11-05-2009 10:56 PM

Cheers
 
Quote:

Originally Posted by wuhoucdc (Post 10112)
Thanks Sci_guy pasted such a great resource!

Also big ups to ECO, Dan, et al. for the Wiki. I've been on the back foot lately in maintaining this list; too busy in the lab. An abstract deadline for the AACR Cancer Epigenetics conference next year to meet :eek:

ohomann 11-11-2009 10:58 AM

Hello everyone,

I was wondering if you would mind adding MochiView, my hybrid genome browser and motif visualization/analysis software, to this list.

Here is a link to the section of the MochiView website with three quick demo videos.

MochiView is particularly useful to anyone interested in identifying/analyzing/managing motifs (multiple motif libraries are available on the MochiView website for import into the software). In addition, members of various labs around UCSF are using the software to visualize/analyze Chip-Chip, Chip-Seq, and RNA-Seq data.

Here are a few more details for those interested:
  • MochiView is desktop Java software with an integrated database
  • MochiView has a rich interface for configuring/saving plot layouts
  • The browser has smooth panning/zooming and a very useful data browsing function
  • MochiView contains a large number of motif utilities, including motif comparison, motif position distribution, motif ROC plots, several motif scoring functions, ability to rapidly export motif scoring of location sets or promoters to spreadsheet, etc.
  • MochiView also contains some Location/Data Set manipulation utilities (e.g. set operations and filters)
  • The website contains a tutorial for download that can familiarize you with many of the basic features
  • MochiView will write and publish your paper for you. OK, that feature isn't quite ready yet

One thing MochiView does NOT do is "peak-calling" for Chip-Chip or Chip-Seq. MochiView leaves this to the many existing solutions and is more appropriate for downstream visualization and analysis.

Thanks for your time,
Oliver Homann
Johnson Laboratory
UCSF

dan 11-11-2009 02:27 PM

Hey Oliver,

I've been working developing the 'wiki arm' of the SEQempire (called SEQwiki) so that it can be used as a browsable / query-able archive of "Software packages for next gen sequence analysis" [1]. The content was seeded from a table on the NBIC wiki [2], which was originally seeded from this list!

It's still work in progress, but the best 'first impression' is probably here:

http://seqwiki.com/wiki/Special:BrowseData


(Lots of packages still need data adding.)

Since setting it up there have been quite a few packages added, mostly by KRobinson but also many others [3]. Please have a go at adding MochiView to the wiki, and let us know how you got on (any good / bad features, etc.).

Cheers,
Dan.

[1] http://seqwiki.com
[2] http://wiki.nbic.nl/index.php/High_t...ncing#Software
[3] http://seqanswers.com/w/index.php?ti...s=30&limit=500 - I still haven't got the query interface working to get proper reports on contributions.


P.S. Perhaps ECO should archive/sticky this thread, create a forum for the wiki and somehow (sticky thread?) let people know to start using the wiki?

ohomann 11-11-2009 03:31 PM

Quote:

Originally Posted by dan (Post 10335)
Hey Oliver,
Please have a go at adding MochiView to the wiki, and let us know how you got on (any good / bad features, etc.).

Hi Dan,

Thanks, I actually found the wiki and added MochiView just after posting to this thread. FWIW, the upload image option doesn't seem to work (it tells me that I don't have a proper extension on my file).

Thanks for the great resource!

ECO 11-11-2009 08:22 PM

Quote:

Originally Posted by dan (Post 10335)

P.S. Perhaps ECO should archive/sticky this thread, create a forum for the wiki and somehow (sticky thread?) let people know to start using the wiki?

I've been considering losing this thread for a while, mainly because any replies in this thread end up emailing about 50% of the members who have either subscribed or posted in the thread (Hi everyone! ;) ).

The second improvement would be to link all these packages to their respective wiki pages.

As a side note, I don't want anyone to get wedded to the new domain seqwiki.com, as the seamless cross-site authentication with the forum accounts does not work. Seqwiki.com is fine for viewing, but wiki.seqanswers.com will be the only one that is editable for a while. (They share the same database). Let's keep this discussion in another thread, perhaps in that "Wiki Development" forum I keep forgetting to set up. :D

Quote:

Originally Posted by ohomann (Post 10337)
Hi Dan,

Thanks, I actually found the wiki and added MochiView just after posting to this thread. FWIW, the upload image option doesn't seem to work (it tells me that I don't have a proper extension on my file).

Thanks for the great resource!

Hmm...perhaps Dan could fix this. ;) :cool:

dan 11-12-2009 01:12 AM

Quote:

Originally Posted by dan (Post 10335)
I still haven't got the query interface working to get proper reports on contributions.

Here is is finally!

The result is pretty awesome! Thanks everyone for taking part!

(I'll break this down to remove 'robot' edits, which is the reason why I currently have so many)

Code:

SELECT
  user_name, user_editcount
FROM
  user
ORDER BY
  user_editcount DESC
;

user_name        user_editcount
Dan                478
Krobison        229
Andreas.sjodin        209
ECO                56
Cariaso        12
Taoliu                5
Maubp                5
Apfejes        4
Nilshomer        4
Simonandrews        4
Weese                4
Wjeck                3
Yxi                3
Ohomann        3
BaCh                3
Dfornika        3
HAA                3
Jkbonfield        2
Ben Langmead        2
Kevleb                2
Joa ds                2
Dawe                2
Balajis        1
Lparsons        1
Jonathan        1
AlwaysSNP        1
Mmartin        1
Lh3                1


Y.Y. LEUNG 11-13-2009 02:41 AM

What is the best Align/Assemble tool?
 
Hi All,

I am a new user of NGS softwares. Thanks a lot for providing such a list. Are there any updates on the information provided?

with so many tools (e.g. in the ALign/assemble field), do anyone has any idea on which tool are the best for use (in terms of ease of usage and computation time required)?

Thanks a lot.

Fanny Leung

dan 11-13-2009 03:00 AM

Quote:

Originally Posted by Y.Y. LEUNG (Post 10407)
Hi All,

I am a new user of NGS softwares. Thanks a lot for providing such a list. Are there any updates on the information provided?

with so many tools (e.g. in the ALign/assemble field), do anyone has any idea on which tool are the best for use (in terms of ease of usage and computation time required)?

I know the feeling!

I'm going to start a 'standard operating procedures' (SOP) section on the wiki to document case studies based on various requirements.

Basically the answer to your question depends on what data you have, what you are trying to do with your data, and what OS you are familiar with. If you can supply those details, I'm sure there will be several suggestions of how to proceed.

wuhoucdc 11-13-2009 08:10 AM

Hi all,

Who have the time to summarize the programs that can be used call SV such as large rearrangement, deletion, amplication among NGS? Thanks.

Wuhoucdc


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