Forum: Pacific Biosciences
09-15-2014, 01:55 AM
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Replies: 12
Views: 6,342
Hi VidJa,
try QUAST...
Hi VidJa,
try QUAST (http://bioinf.spbau.ru/quast). It's a pretty handy tool for doing both statistical and biological evaluation of assemblies. It has a web interface but alternatively you can...
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Forum: Pacific Biosciences
05-26-2014, 01:29 AM
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Replies: 20
Views: 5,774
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Forum: Pacific Biosciences
05-19-2014, 01:43 AM
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Replies: 20
Views: 5,774
Hi wrch,
you may want to consider generating...
Hi wrch,
you may want to consider generating PacBio CCS reads, rather than CLR. The CCS reads have a much lower error rate (somehwhere between 1 and 3% usually). This comes at the expense of...
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Forum: Bioinformatics
01-06-2014, 03:11 AM
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Replies: 2
Views: 1,204
Hi Ramesh,
try Strudel --...
Hi Ramesh,
try Strudel -- http://bioinf.hutton.ac.uk/strudel/. It's easy to install as it comes with prebuilt installers for all major platforms. It uses its own data format, which will cost you a...
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Forum: Bioinformatics
11-11-2013, 01:45 AM
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Replies: 5
Views: 1,638
The head command in Linux also alllows you to...
The head command in Linux also alllows you to extract a number of lines from the start of the file (or use the tail command for the end of the file), without splitting the whole file:
In analogy...
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Forum: Bioinformatics
08-26-2013, 01:12 AM
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Replies: 1
Views: 1,309
Hi Petrichor,
by default BLAST hits with...
Hi Petrichor,
by default BLAST hits with multiple HSPs to the same subject are sorted by bit score in descending order, i.e. the best (and usually longest) HSP is topmost.
Here is what I have...
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Forum: Bioinformatics
08-19-2013, 03:03 AM
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Replies: 4
Views: 2,592
Hi Henrik,
try Strudel...
Hi Henrik,
try Strudel (http://bioinf.hutton.ac.uk/strudel/) -- this may be just what you are after.
I was the main developer on Strudel while it was actively being developed, but we now don't...
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Forum: RNA Sequencing
03-25-2013, 04:13 AM
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Replies: 0
Views: 2,508
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Forum: RNA Sequencing
03-25-2013, 02:51 AM
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Replies: 3
Views: 2,700
Hi Homa,
duplicates are a fact of life with...
Hi Homa,
duplicates are a fact of life with RNASeq. In fact, we regularly see 80-90% duplication in our RNASeq here. I always remove duplicates before SNP calling as it reduces the false positive...
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Forum: RNA Sequencing
03-25-2013, 02:47 AM
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Replies: 12
Views: 4,193
Hi galata44,
what software have you used for...
Hi galata44,
what software have you used for assembling the transcripts? If you used a dedicated transcriptome assembler your clusters of similar transcripts probably represent alternative splice...
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Forum: Bioinformatics
03-04-2013, 01:54 AM
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Replies: 1
Views: 1,498
Hi k2bhide,
here are a couple of things to...
Hi k2bhide,
here are a couple of things to try:
- try the mpileup without the -B option, in case this is filtering out SNPs
- try without the filtering script
- set the minimum base quality...
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Forum: Bioinformatics
02-26-2013, 02:15 AM
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Replies: 17
Views: 33,003
Hi nr23,
the individual lines in your BLAST...
Hi nr23,
the individual lines in your BLAST output are HSPs (high-scoring segment pairs). You can have several of these per query-hit combination. They represent local stretches of aligned...
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Forum: Bioinformatics
02-26-2013, 02:00 AM
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Replies: 1
Views: 3,142
Hi smriti,
you have come to the right place!...
Hi smriti,
you have come to the right place! :) Have a look at the how-to section of the Seqanswers wiki pages:
http://seqanswers.com/wiki/How-to
There are also nice explanations of the...
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Forum: RNA Sequencing
02-26-2013, 01:52 AM
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Replies: 11
Views: 2,325
Hi rohitngs,
if your genomic assembly is...
Hi rohitngs,
if your genomic assembly is fairly complete you could try to map the reads onto that (combine the contigs and scaffolds into a single FASTA file and index that for Bowtie).
In...
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Forum: Bioinformatics
01-21-2013, 01:58 AM
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Replies: 9
Views: 1,817
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Forum: De novo discovery
10-29-2012, 02:55 AM
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Replies: 11
Views: 6,575
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Forum: De novo discovery
10-22-2012, 02:16 AM
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Replies: 11
Views: 6,575
Hi,
2 and 3 sound reasonable. As to point...
Hi,
2 and 3 sound reasonable. As to point 1), I wouldn't exclude transcripts on the basis of being lowly expressed -- you may end up removing genuine transcripts from your final set. Remember that...
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Forum: Bioinformatics
10-22-2012, 02:10 AM
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Replies: 3
Views: 1,296
Hi mht,
I have little experience of how...
Hi mht,
I have little experience of how Bowtie would handle mapping reads onto scaffolded sequences with Ns in them, but does this still happen if you force the reads to have, say, no more than 1...
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Forum: Bioinformatics
10-15-2012, 03:35 AM
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Replies: 3
Views: 1,296
Hi mht,
we work on plants here too and I...
Hi mht,
we work on plants here too and I tend to use Bowtie for my mapping (= reference assembly). Of all the mappers I have tried it gives me the greatest degree of control. It has this great...
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Forum: De novo discovery
10-15-2012, 03:02 AM
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Replies: 11
Views: 6,575
Hi,
personally I think that looks...
Hi,
personally I think that looks reasonable, assuming you have a eukaryotic organism -- the average gene length in eukaryotes is supposed to be in the 1,500 bp region. What organism is this, and...
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Forum: Bioinformatics
10-15-2012, 02:21 AM
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Replies: 1
Views: 1,560
Hi ElDonnis,
is the M. truncatula genome...
Hi ElDonnis,
is the M. truncatula genome sequenced?
I would probably take the following approach for your sativa data:
1. De novo assembly of the RNASeq with e.g. Trinity
2. Meta-assembly...
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Forum: Bioinformatics
10-01-2012, 02:04 AM
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Replies: 5
Views: 2,330
Hi Jon,
try Tablet...
Hi Jon,
try Tablet (http://bioinf.scri.ac.uk/tablet/). It takes ace files and you can import annotation as tracks in GFF format (if you have annotation in your GTF file you may need to tweak this...
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Forum: Bioinformatics
09-17-2012, 01:51 AM
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Replies: 6
Views: 5,413
Hi Rahul,
try Strudel...
Hi Rahul,
try Strudel (http://bioinf.scri.ac.uk/strudel/) -- it might do the trick for you, and it looks pretty in a publication. It's perhaps better suited for doing comparisons at the chromosome...
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Forum: RNA Sequencing
08-27-2012, 02:26 AM
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Replies: 3
Views: 1,409
Hi rndouglas,
it sounds like SeqTrimMap is...
Hi rndouglas,
it sounds like SeqTrimMap is suppressing anything that isn't small RNA.
Here is what I would do:
1. Convert the SAM file that SeqTrimMap produced to BAM format.
2. Extract...
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Forum: Bioinformatics
06-04-2012, 01:36 AM
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Replies: 1
Views: 1,562
Hi lg36,
you're not wrong about this at all...
Hi lg36,
you're not wrong about this at all -- this is in fact a pretty important factor in SNP discovery.
Your SNPs can only ever be as good as your reference and your mapping. If your...
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