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Forum: Bioinformatics 09-16-2015, 05:22 AM
Replies: 1
Views: 1,237
Posted By darked89
The CPC site is up again. And the info about...

The CPC site is up again. And the info about installation is here:
http://cpc.cbi.pku.edu.cn/docs/install_guide.jsp

I have not used it on the command line for a while but remember that some input...
Forum: Bioinformatics 09-15-2015, 03:24 PM
Replies: 8
Views: 1,804
Posted By darked89
Well, catching up with htslib is one thing, but...

Well, catching up with htslib is one thing, but going from test BAM with

@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:1000


towards one where one can:
* create BAM with real world header taken...
Forum: Bioinformatics 09-15-2015, 02:00 PM
Replies: 8
Views: 1,804
Posted By darked89
Just a short tip taken from dpryan earlier post,...

Just a short tip taken from dpryan earlier post, but somehow not popping up in google results on top how to compile the above code snippets:

gcc -Wall -o mysnippet mysnippet.c -lbam -lz...
Forum: Bioinformatics 11-17-2014, 10:39 AM
Replies: 1
Views: 1,342
Posted By darked89
From the error it seems that it looks for...

From the error it seems that it looks for "genes.gff" and not "genes.gff3". Just link it and see if it works,
Forum: Bioinformatics 11-10-2014, 05:50 AM
Replies: 4
Views: 1,416
Posted By darked89
CEGMA in Docker

There is a Docker container for CEGMA:
https://registry.hub.docker.com/u/robsyme/cegma-docker/

So instead of installing each component on its own one can just install Docker, execute few commands...
Forum: Bioinformatics 02-11-2014, 09:36 AM
Replies: 2
Views: 2,110
Posted By darked89
Yes. Just run the last command without the -Wl ...

Yes. Just run the last command without the -Wl
Like this:

g++ `python2.7-config --ldflags` -pthread -shared build/linux-x86_64-2.7-ucs4/pyx/maptools.o build/linux-x86_64-2.7-ucs4/c/maputils.o...
Forum: Bioinformatics 07-31-2012, 07:17 AM
Replies: 14
Views: 2,323
Posted By darked89
Hard to tell why. Few ideas: 1) Just in...

Hard to tell why. Few ideas:

1) Just in case: you are using sorted and indexed BAM as SRMA input?

2) Try to get some small test BAM file which is known to run OK with SRMA and then check if...
Forum: Bioinformatics 07-24-2012, 11:41 AM
Replies: 14
Views: 2,323
Posted By darked89
Source on github seems to be newer, but still 1...

Source on github seems to be newer, but still 1 year old:

https://github.com/nh13/SRMA
Forum: Bioinformatics 07-24-2012, 09:53 AM
Replies: 7
Views: 1,568
Posted By darked89
Few tips: 1) error correction prior to...

Few tips:

1) error correction prior to assembly
I used Coral (5 iterations) but you may check Quake or Reptile

2) depending on insert sizes of your libs, you may try to find overlaps between...
Forum: Bioinformatics 01-27-2012, 05:45 AM
Replies: 1
Views: 4,724
Posted By darked89
GSNAP is what you can use for spliced mapping of...

GSNAP is what you can use for spliced mapping of Illumina 50bp single-end reads. The default output is SAM. With 50bp you will have some problems with reads spanning splice junctions, so you may be...
Forum: Bioinformatics 01-27-2012, 05:32 AM
Replies: 9
Views: 2,501
Posted By darked89
You may try LAST: http://last.cbrc.jp/ It...

You may try LAST: http://last.cbrc.jp/
It accepts fastq format, outputs MAF, which then you can convert to SAM/BAM.
Forum: Bioinformatics 09-08-2011, 08:18 AM
Replies: 9
Views: 20,869
Posted By darked89
I managed to run: ./gene2xml.linux -i...

I managed to run:

./gene2xml.linux -i Sus_scrofa.ags -b T -c T

This prints XML output. Strangely Sus_scrofa.ags had to be gzipped and named Sus_scrofa.ags.gz.

XML to gff convertion should...
Forum: SOLiD 08-16-2011, 06:18 AM
Replies: 6
Views: 4,501
Posted By darked89
Same for FASTQ format. Maybe there is something...

Same for FASTQ format. Maybe there is something to be gained from color 2 fasta conversion and mapping by blat.



Also you may try to use CEGMA (http://korflab.ucdavis.edu/Datasets/cegma/)...
Forum: SOLiD 08-15-2011, 07:23 AM
Replies: 0
Views: 1,134
Posted By darked89
SOLID split RNA-Seq mapping

I got few SOLID RNA-Seq files which I am trying to map to some "draft+ quality" mammalian genome. So far I tried:

bowtie 0.12.7 (unspliced mode)
tophat 1.3.1 (spliced)
ab_wtp_1.2.1...
Forum: SOLiD 08-15-2011, 07:16 AM
Replies: 6
Views: 4,501
Posted By darked89
Augustus can cope with "hints" created by mapping...

Augustus can cope with "hints" created by mapping Illumina reads (converted to fasta) with splice-agnostic blat. So as long as you have some gene models for training, unspliced mappings should work,...
Forum: Bioinformatics 07-13-2011, 08:07 AM
Replies: 6
Views: 2,253
Posted By darked89
Get the newest version of (samtools 0.1.17), and...

Get the newest version of (samtools 0.1.17), and convert the SAM to sorted BAM, preferably with index.
Forum: Bioinformatics 05-23-2011, 02:14 AM
Replies: 5
Views: 1,020
Posted By darked89
1) what was the command line you used to run...

1) what was the command line you used to run tophat?
2) tophat creates (unless modified) tophat_out directory with logs/ and tmp/ subdirs.
What is the content of tophat_out/logs/run.log?
3)...
Forum: Bioinformatics 04-07-2011, 06:36 AM
Replies: 3
Views: 2,696
Posted By darked89
AUGUSTUS is able to use RNA-Seq data and did a...

AUGUSTUS is able to use RNA-Seq data and did a good job at gene prediction (at least in one plant genome). Problem is, one has to map reads using blat, which is not weapon of choice for fast and...
Forum: RNA Sequencing 11-26-2010, 07:45 AM
Replies: 29
Views: 11,845
Posted By darked89
Hi proteomania, many thanks for answering. ...

Hi proteomania,

many thanks for answering.

One last thing: can mix reads with various lengths? I got 54 & 76bp reads.
Forum: RNA Sequencing 11-26-2010, 02:13 AM
Replies: 29
Views: 11,845
Posted By darked89
@mdimon I have few lanes of paired RNA-Seq...

@mdimon

I have few lanes of paired RNA-Seq reads from few tissues (plant, novel genome). Do you recommend concatenating all of them into a single giant file, or running individual lanes, or even...
Forum: Bioinformatics 11-18-2010, 07:53 AM
Replies: 1
Views: 4,763
Posted By darked89
Just found the answer in another thread: ...

Just found the answer in another thread:

http://seqanswers.com/forums/showpost.php?p=16265&postcount=27
Forum: Bioinformatics 11-18-2010, 06:39 AM
Replies: 1
Views: 4,763
Posted By darked89
Question tophat/cufflinks for novel genome annotation

I got a novel plant genome in an advanced draft phase and 8 Illumina paired RNA-Seq lanes, The RNA-Seq data is mostly from other strains, and the read lengths differ between lanes.
The goal is to...
Forum: Bioinformatics 06-10-2010, 09:40 AM
Replies: 39
Views: 15,901
Posted By darked89
Here is a recipe how to install and run...

Here is a recipe how to install and run RepeatScout:

http://openwetware.org/wiki/Wikiomics:Repeat_finding#RepeatScout

Hope it helps,

Darek
Forum: Bioinformatics 05-03-2010, 03:32 AM
Replies: 1
Views: 3,470
Posted By darked89
Question SAM format: single vs multiple hits

According to the specification, there is SAM flag:
0x0100 0x0100 "the alignment is not primary (a read having split hits may have multiple primary alignment records)"

but using...
Forum: Bioinformatics 05-01-2010, 05:19 AM
Replies: 35
Views: 15,695
Posted By darked89
Question I am also getting seed lengths = read_length (54,...

I am also getting seed lengths = read_length (54, 76bp). Tophat runs fine till the end, but the accepted_hits.sam has zero spliced reads (for 76bp run). I run it in paired end mode, therefore assumed...
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