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Forum: Pacific Biosciences 09-15-2014, 12:55 AM
Replies: 12
Views: 6,199
Posted By mbayer
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...
Forum: Pacific Biosciences 05-26-2014, 12:29 AM
Replies: 20
Views: 5,569
Posted By mbayer
My experience of this has been that the CCS reads...

My experience of this has been that the CCS reads - even though they are short by comparison with CLR - complement the Illumina reads nicely and bridge a lot of the gaps between contigs that have...
Forum: Pacific Biosciences 05-19-2014, 12:43 AM
Replies: 20
Views: 5,569
Posted By mbayer
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...
Forum: Bioinformatics 01-06-2014, 02:11 AM
Replies: 2
Views: 1,167
Posted By mbayer
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...
Forum: Bioinformatics 11-11-2013, 12:45 AM
Replies: 5
Views: 1,585
Posted By mbayer
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...
Forum: Bioinformatics 08-26-2013, 12:12 AM
Replies: 1
Views: 1,245
Posted By mbayer
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...
Forum: Bioinformatics 08-19-2013, 02:03 AM
Replies: 4
Views: 2,532
Posted By mbayer
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...
Forum: RNA Sequencing 03-25-2013, 03:13 AM
Replies: 0
Views: 2,482
Posted By mbayer
High concentration of read errors in reverse orientation reads

Hi,

I have a bizarre problem with what looks like read errors that occur predominantly at the end of reverse orientation reads (i.e. at the read start on forward orientation). My reads are 101bp...
Forum: RNA Sequencing 03-25-2013, 01:51 AM
Replies: 3
Views: 2,647
Posted By mbayer
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...
Forum: RNA Sequencing 03-25-2013, 01:47 AM
Replies: 12
Views: 4,052
Posted By mbayer
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...
Forum: Bioinformatics 03-04-2013, 12:54 AM
Replies: 1
Views: 1,438
Posted By mbayer
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...
Forum: Bioinformatics 02-26-2013, 01:15 AM
Replies: 17
Views: 31,856
Posted By mbayer
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...
Forum: Bioinformatics 02-26-2013, 01:00 AM
Replies: 1
Views: 3,096
Posted By mbayer
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...
Forum: RNA Sequencing 02-26-2013, 12:52 AM
Replies: 11
Views: 2,212
Posted By mbayer
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...
Forum: Bioinformatics 01-21-2013, 12:58 AM
Replies: 9
Views: 1,763
Posted By mbayer
Hi yaximik, I use this in my bash scripts: ...

Hi yaximik,

I use this in my bash scripts:


#extract all the filenames to an array
files=`ls -l *.gz | awk '{ print $9 }'`

#iterate over these
for i in $files
Forum: De novo discovery 10-29-2012, 01:55 AM
Replies: 11
Views: 6,463
Posted By mbayer
I would not set a cut-off at all. Like I said, I...

I would not set a cut-off at all. Like I said, I don't think you can assume that a low expression level means there is an artefact -- it could be real.

Micha
Forum: De novo discovery 10-22-2012, 01:16 AM
Replies: 11
Views: 6,463
Posted By mbayer
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...
Forum: Bioinformatics 10-22-2012, 01:10 AM
Replies: 3
Views: 1,263
Posted By mbayer
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...
Forum: Bioinformatics 10-15-2012, 02:35 AM
Replies: 3
Views: 1,263
Posted By mbayer
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...
Forum: De novo discovery 10-15-2012, 02:02 AM
Replies: 11
Views: 6,463
Posted By mbayer
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...
Forum: Bioinformatics 10-15-2012, 01:21 AM
Replies: 1
Views: 1,507
Posted By mbayer
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...
Forum: Bioinformatics 10-01-2012, 01:04 AM
Replies: 5
Views: 2,255
Posted By mbayer
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...
Forum: Bioinformatics 09-17-2012, 12:51 AM
Replies: 6
Views: 5,306
Posted By mbayer
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...
Forum: RNA Sequencing 08-27-2012, 01:26 AM
Replies: 3
Views: 1,357
Posted By mbayer
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...
Forum: Bioinformatics 06-04-2012, 12:36 AM
Replies: 1
Views: 1,504
Posted By mbayer
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...
Showing results 1 to 25 of 29

 


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