User: burnsro

gravatar for burnsro
burnsro20
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20
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New User
Location:
Austria
Last seen:
3 years ago
Joined:
5 years, 1 month ago
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b******@tcd.ie

Posts by burnsro

<prev • 12 results • page 1 of 2 • next >
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Comment: C: condition bedtools on name column
... File A and File B are a general example, but ideally I'd like to scale up to many FileAs and FileBs. I agree your way works its just a lot of intermediates to generate. ...
written 3.1 years ago by burnsro20
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Comment: C: condition bedtools on name column
... Yes I understood what you meant by using grep in the first comment, but it would lead to a lot of pairwise comparisons to make especially with many bed files to compare. With bedtools you can use one file to compare with many at once, thats why I wrote it in the question. ...
written 3.1 years ago by burnsro20
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Comment: C: condition bedtools on name column
... It would work. I am only hesitant to use something other than bedtools because bedtools has many useful option such as -c to count the number of files that has an interval, -f for matching only a percentage of an interval, -wa and -wb etc. ...
written 3.1 years ago by burnsro20
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Comment: C: condition bedtools on name column
... True, it would just be a lot of "grepped" files to make for each unique name in column4. This example I made is just simplification. ...
written 3.1 years ago by burnsro20
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condition bedtools on name column
... Bedtools accepts files with formats like 'chr start end name score strand' However, is it possible to take these columns into account (e.g name column) when using bedtools intersect or bedtools merge. For example I have a bed file like so, with a 'name' column for transposable elements FileA: ...
bedtools written 3.1 years ago by burnsro20 • updated 3.1 years ago by Alex Reynolds28k
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RepeatMasker on new species
... I have run RepeatMasker on a species of arabidopsis, using a personal library, however in the tbl output it tells me The query species was assumed to be homo RepeatMasker version open-4.0.5 , default mode I cannot change -species command and use a personal library, -lib, at the same time to run Re ...
transposons written 4.1 years ago by burnsro20 • updated 8 weeks ago by predeus1.2k
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Comment: C: Transposons and Pacbio
... I was planning to do de novo assembly, and infer repeats from the reads ...
written 4.2 years ago by burnsro20
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Transposons and Pacbio
... What tools are available to call TEs using Pacbio data? My understanding is that most work using paired-end reads from short read Illumina data. ...
pacbio written 4.2 years ago by burnsro20 • updated 4.2 years ago by nterhoeven80
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Make pairwise fasta file for two species
... I have a fasta file of DNA sequences for two different species across a chromosome, e.g. >SpeciesA_gene1 ACTGC..... and  >SpeciesB_geneX TCTGC... and a text file of orthologs SpeciesA SpeciesB gene1 geneX (etc)   I want to assign each ortholog pair into a seperate file, so I ...
fasta clustal written 4.3 years ago by burnsro20 • updated 4.3 years ago by tomc80
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Making fasta file for clustal
... I have two fasta files of DNA sequences for upstream promoter regions for two species, and I would like to align them in clustalW I read on the clustalW manual pages in ubuntu that "all sequences must be in 1 file, one after another" I'm trying to understand if that means I need to have each ortho ...
fasta clustal written 4.3 years ago by burnsro20 • updated 4.3 years ago by Charles Plessy2.7k

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