User: dzisis1986

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dzisis198620
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Posts by dzisis1986

<prev • 84 results • page 1 of 9 • next >
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Comment: C: Problem in visualizing bam files to IGV
... Yes i know so my bam files are in the correct format for my reference ,fa as i described above ! This sed doesnt work for my bam file it destroys the format and i cant view it with samtools ! ...
written 5 months ago by dzisis198620
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Problem in visualizing bam files to IGV
... Hi I have my sorted bam files like that : bedtools genomecov -ibam Ath_FLC4C_A_2_sorted.bam -bg | head 1:13169-20070() 0 28 13 1:20064-28278() 1733 1761 441 1:28272-29965() 1665 1693 332 1:29959-36604() 3964 3992 367 1:52850-54453() 1575 1603 1523 1:83123-87907() 4756 ...
bam view igv written 5 months ago by dzisis198620
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(Closed) Check values in columns of a window of fragments and return new table based on condition in R
... I have a table like this : V1 V2 V3 V4 V5 V6 V7 V8 V9 1 1 7512 1 0 0 0 0 0 1 7506 10949 0 0 0 0 0 1 1 10943 13175 0 0 0 0 0 0 1 13169 20070 0 1 1 0 0 0 Each line in the table is a fragment so the fragnum is 4. Con1 includes ...
table R column fragments written 7 months ago by dzisis198620
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Comment: C: Merge overlapping intervals in a bed file containing different chromosomes
... i used different sort command like sortBed -i and also sort -n -k1.11 -nk2,2 . but still the same problem ! ...
written 8 months ago by dzisis198620
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Comment: C: Merge overlapping intervals in a bed file containing different chromosomes
... I already did this but something is wrong with sort , maybe the fact that there are different chr and when i use bedtools merge i have an error like : Error: Sorted input specified, but the file sorted.bed has the following out of order record chr5 3700000 3899999 0 0.013255902570394 ...
written 8 months ago by dzisis198620
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Merge overlapping intervals in a bed file containing different chromosomes
... Hello I have a file test.bed like this : chr2 3300000 3499999 0 0.013255902570394 chr3 300000 499999 0 0.015744466292456 chr4 9400000 9599999 0 0.045555030342908 chr5 1700000 1899999 0 0.013255902570394 chr5 23900000 24099999 0 0.037583056937021 c ...
bed merge script written 8 months ago by dzisis198620 • updated 8 months ago by Pierre Lindenbaum128k
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Comment: C: How can I reproduce features of signalp TMHMM and phobius?
... thank you for the detailed description and the the example. i already checked the posibilites in uniprot and i do believe that the existing programs are giving the best results . I am just trying to see if and how can be possible to do something similar without them. i agree that you need a lot of t ...
written 9 months ago by dzisis198620
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Comment: C: How can I reproduce features of signalp TMHMM and phobius?
... I know that those programs are predicting those features in a good way. i am just trying to extract some different features from different programs in the simplest way and thenuse them for further machine learning analysis. i want to use as input a fasta with protein sequences and be able to have a ...
written 9 months ago by dzisis198620
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Comment: C: How can I reproduce features of signalp TMHMM and phobius?
... I read the papers describing the programs carefully and i found more or less how some of the features are calculated but i can't until now understand clearly how those are in practice. i would like to calculate some basic features like presence of signal peptide or existence of transmembrane helice ...
written 9 months ago by dzisis198620
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How can I reproduce features of signalp TMHMM and phobius?
... Is it possible to use a fasta with protein sequences to predict signal peptide and TM without using signap, TMHMM, phobius ? How can i reproduce- calculate information about signal peptide presence or number of transmembrane helices ? I would like to get similar results like the features Phobius_TM ...
transmembrane signal peptide tm written 9 months ago by dzisis198620 • updated 9 months ago by Mensur Dlakic5.5k

Latest awards to dzisis1986

Supporter 19 months ago, voted at least 25 times.
Popular Question 24 months ago, created a question with more than 1,000 views. For Bowtie 2: bowtie build does not create .rev index files
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Bowtie 2: bowtie build does not create .rev index files

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