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Search: Posts Made By: Thorondor
Forum: Bioinformatics 03-26-2015, 09:47 AM
Replies: 28
Views: 60,373
Posted By Thorondor
found this thread and decided to revive it. Did...

found this thread and decided to revive it.
Did anyone tried to get back to several fastq pairs r1 and r2 merged into one bam file. Alignment was done with bwa mem, merging with biobambam.
3...
Forum: Bioinformatics 09-18-2012, 12:15 AM
Replies: 8
Views: 11,757
Posted By Thorondor
one question, if I have read pairs does it for...

one question, if I have read pairs does it for sampe if I switch read pairs for the input?

like:
bwa sampe ref.fa 2.sai 1.sai read2.fq read1.fq > aln.sam

instead of:
bwa sampe ref.fa 1.sai...
Forum: Bioinformatics 07-06-2012, 01:50 AM
Replies: 1
Views: 1,102
Posted By Thorondor
when does BWA writes the outpu .sai

This might be a dumb question, but I can't find the answer anywhere and also don't have to possibility to test it right now.
When does BWA wrirte the output to the *.sai file?
Is it happening on...
Forum: De novo discovery 09-19-2011, 06:50 AM
Replies: 8
Views: 12,496
Posted By Thorondor
I am working with illumina reads (PE 100bp). ...

I am working with illumina reads (PE 100bp).

well the minimum kmer coverage is default 1 for trinity for oases it is 3, so maybe results will be better with trinity. but of course a lot depends on...
Forum: De novo discovery 09-15-2011, 01:47 AM
Replies: 8
Views: 12,496
Posted By Thorondor
i did assemble an eukaryotic transcriptome with...

i did assemble an eukaryotic transcriptome with oases and also with trinity. And as far as i did check the results there are high similarities and it is not easy to say which assembly is strictly...
Forum: De novo discovery 06-28-2011, 03:11 AM
Replies: 58
Views: 50,897
Posted By Thorondor
yup, this happens also for me, scaffolding is off...

yup, this happens also for me, scaffolding is off per default in oases and but you still get this Ns because oases still connect read pairs.

zerbino wrote over oases mailinglist:
"scaffolding...
Forum: Bioinformatics 05-21-2011, 02:44 AM
Replies: 31
Views: 10,012
Posted By Thorondor
yup Jenzo, also did get this email, but the oases...

yup Jenzo, also did get this email, but the oases compilation bug "src/readSet.c:34: fatal error: zlib.h: File or directory not found compilation terminated." is still there. ;-)
Forum: Bioinformatics 05-20-2011, 10:27 AM
Replies: 31
Views: 10,012
Posted By Thorondor
you can copy the *.o files in ...

you can copy the *.o files in third-party/zlib-1.2.3 from an older velvet version. I am pretty sure that they did not changed.
Forum: De novo discovery 05-11-2011, 06:13 AM
Replies: 58
Views: 50,897
Posted By Thorondor
on the oases malinglist Daniel Zerbino wrote: ...

on the oases malinglist Daniel Zerbino wrote:
"Are you compiling Oases with the OPENMP flag? This indeed is not allowed
by the Oases Makefile, as Oases will not be accelerated by the parallel ...
Forum: De novo discovery 05-04-2011, 11:19 AM
Replies: 16
Views: 6,886
Posted By Thorondor
yes, it is the first hit when you google...

yes, it is the first hit when you google "definition: N50"

separate to "shortpaired" I assume. So you can use 2 different PE libraries with different insert sizes, but maybe I am wrong.

Total...
Forum: Bioinformatics 05-04-2011, 03:48 AM
Replies: 2
Views: 1,342
Posted By Thorondor
http://toolkit.tuebingen.mpg.de/sections/alignment...

http://toolkit.tuebingen.mpg.de/sections/alignment

take a look, have fun. ;-)
Forum: RNA Sequencing 05-04-2011, 02:48 AM
Replies: 12
Views: 3,929
Posted By Thorondor
no, i don't think that the non-normalisation is...

no, i don't think that the non-normalisation is the reason here, but keep in mind that you coverage is not consistent over all transcripts. So it might get some transcripts better assembled with a...
Forum: RNA Sequencing 05-04-2011, 01:54 AM
Replies: 12
Views: 3,929
Posted By Thorondor
so what exactly is your question? This sounds all...

so what exactly is your question? This sounds all reasonable to me. You have a comparison to a normalized library? What is your expected coverage? And kmer 29 might be bit high if your calculated...
Forum: De novo discovery 05-04-2011, 01:47 AM
Replies: 16
Views: 6,886
Posted By Thorondor
come on, do a bit more research on your own. :P ...

come on, do a bit more research on your own. :P

read the velvet paper:
http://genome.cshlp.org/content/18/5/821.short

You don't want to use the graph and if you know what a graph is you should...
Forum: De novo discovery 05-02-2011, 09:21 AM
Replies: 8
Views: 5,107
Posted By Thorondor
well if your genes of interested are not well...

well if your genes of interested are not well covered you might also take a look at LOCAS for your assembly:
http://ab.inf.uni-tuebingen.de/software/locas/
Forum: Bioinformatics 05-02-2011, 09:15 AM
Replies: 10
Views: 5,056
Posted By Thorondor
so why not trim the reads first and then try to...

so why not trim the reads first and then try to map without quality values? You don't want to assemble bad reads anyway and they mostly won't overlap if you don't trim. Or you could just cut all your...
Forum: Bioinformatics 05-02-2011, 02:08 AM
Replies: 10
Views: 5,056
Posted By Thorondor
if you have illulmina reads you might want to...

if you have illulmina reads you might want to read this review:
http://seqanswers.com/forums/showthread.php?t=11045
Forum: Bioinformatics 05-02-2011, 01:19 AM
Replies: 10
Views: 5,056
Posted By Thorondor
amount of reads? size of your reference genome?...

amount of reads? size of your reference genome? what software you tried already?
Forum: De novo discovery 05-02-2011, 01:17 AM
Replies: 8
Views: 5,107
Posted By Thorondor
so you have references of your genes you are...

so you have references of your genes you are looking for and what %-identity you expect in the sequence? Blasting all your reads against your reference genes seems not to be the smartest way. ;-)...
Forum: De novo discovery 04-28-2011, 03:58 AM
Replies: 16
Views: 6,886
Posted By Thorondor
i have no clue what genegenious is and on what...

i have no clue what genegenious is and on what algorithm it is based. So if it is a ovelap-based method, yes it is possible and depends on kmer, amount of reads you have, expected coverage, read...
Forum: De novo discovery 04-28-2011, 12:17 AM
Replies: 16
Views: 6,886
Posted By Thorondor
http://brianknaus.com/software/srtoolbox/fastq2fas...

http://brianknaus.com/software/srtoolbox/fastq2fasta.pl

first hit in google. ;-) Also normally trimming "programs" takes fastq as input and output a fasta.

velvet needs a good coverage to do...
Forum: De novo discovery 04-26-2011, 08:25 AM
Replies: 16
Views: 6,886
Posted By Thorondor
sure there are a lot of ways. ;-) Use a script,...

sure there are a lot of ways. ;-) Use a script, you even have the (length + kmer -1) in the id of the contig so it is really easy.

here are some perl scripts that might help:...
Forum: De novo discovery 04-26-2011, 02:17 AM
Replies: 16
Views: 6,886
Posted By Thorondor
if you don't want to compare paired end to single...

if you don't want to compare paired end to single end you don't need to do "subsetting".

the last line just tells you your N50, how many reads were used (you can also request velvet to output a...
Forum: De novo discovery 04-20-2011, 08:50 AM
Replies: 58
Views: 50,897
Posted By Thorondor
depending on your number of reads it takes...

depending on your number of reads it takes "hours" till it finishes.

5hours
30GB RAM
with around 70.000.0000 reads with average length 90

you can speed things up with the new parallel mode...
Forum: RNA Sequencing 04-20-2011, 01:17 AM
Replies: 12
Views: 3,929
Posted By Thorondor
Well it should work fine I guess especially for...

Well it should work fine I guess especially for the high expressed transcripts. But I can't say that for sure since I am working with Illumina reads.
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