User: Pawel Osipowski

Reputation:
20
Status:
New User
Location:
Poland, Warsaw
Website:
http://csgenome.sggw.p...
Last seen:
9 months, 3 weeks ago
Joined:
4 years, 4 months ago
Email:
p*********@gmail.com

Posts by Pawel Osipowski

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Plotting Density Of Snps On Chromosomes
... I know this is old and something could change in libraries but is there anybody to help with that error message when trying to recreate this: `Error: StatBin requires a continuous x variable the x variable is discrete. Perhaps you want stat="count"?` Thanks in advance ...
written 10 months ago by Pawel Osipowski20
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Answer: A: pbalign issue: blasr v5.1 seems to be not integrated with pbalign
... It looks like they fixed this issue by producing blasr v5.3. You have to install pbalign and blasr through their new installing platform called pitchfork. From my experience be very careful using clean environment they offer. Right now I'm trying to get back to my system environment after I terminat ...
written 2.5 years ago by Pawel Osipowski20
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Comment: C: pbalign issue: blasr v5.1 seems to be not integrated with pbalign
... It seems they work on this. Some additional info is here: https://github.com/PacificBiosciences/pbalign/issues/48 ...
written 2.5 years ago by Pawel Osipowski20
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Comment: C: pbalign issue: blasr v5.1 seems to be not integrated with pbalign
... It's horrible experience to me too :) especially from half a year ago when I was doing it on an old system. I followed those recently: https://github.com/PacificBiosciences/pbalign/blob/master/doc/howto.rst https://github.com/PacificBiosciences/blasr/wiki/Step-by-step-blasr-installation-example you ...
written 2.5 years ago by Pawel Osipowski20
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pbalign issue: blasr v5.1 seems to be not integrated with pbalign
... When installing the newest blasr and pbalign through github tutorials I get this after running pbalign. ERROR: --sam is no longer supported, use --bam, then translate from .bam to .sam [ERROR] 2016-09-10 11:00:09,126Z [root Execute 67] BlasrService returned a non-zero exit status. [INFO] 20 ...
alignment pbalign blasr pacbio written 2.5 years ago by Pawel Osipowski20
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Answer: A: Whole genome coordinates of promoters/gene regulatory elements
... For other species, as this is the only post considered promoters, a useful tool might be 'bedtools flank'. From bed/gff/gtf you can produce file with intervals flanking start codon. I did this to generate gtf with promoter sequence intervals reaching 500nt downstream and 1000 upstream from a start_c ...
written 2.7 years ago by Pawel Osipowski20
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Comment: C: merge two mulitfasta files and eliminate fasta with duplicated headers from the
... Great thanks Jorge, very neat solution. Do you think there might be some problems with ends of the last lines in files? Repeatmasker says some headers are too long but they shouldn't be. There is over 6k sequences and I'm slow at scripting. ...
written 2.7 years ago by Pawel Osipowski20
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Comment: C: merge two mulitfasta files and eliminate fasta with duplicated headers from the
... Hi Brian, first of all you've got my deep admiration for tools you produced. I'm using it since one year! When any paper is comming? I would cite with pleasure! Your method worked best because without any additional check repeatmasker swallowed converted first multifasta opposed to two other methods ...
written 2.7 years ago by Pawel Osipowski20
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merge two mulitfasta files and eliminate fasta with duplicated headers from the first
... Hi, I have two multifasta files. I want to merge them deleting all those fasta seqences from the first multifasta file which are also in the second file. I need to do it by header comparison, sequences are different under the same headers. Alternatively, could somebody give me a hint how to generat ...
genome assembly sequence bcftools fasta written 2.7 years ago by Pawel Osipowski20 • updated 2.7 years ago by Jorge Amigo11k
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Comment: C: Breakdancer: bam2cfg.pl error
... ... and you can do this by 'bamaddrg' e.g. ...
written 2.8 years ago by Pawel Osipowski20

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