User: rah

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rah20
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Posts by rah

<prev • 14 results • page 1 of 2 • next >
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Gene Annotation in Bed file
... Hi All, I'm currently working with a bunch of bed files containing specific regions of the human genome. I wish to annotate the regions with genes, and especially genes related to man. However, to do this, I need a bedfile with the coordinates for each gene and a proper naming for that gene in or ...
gene annotation disease written 8 weeks ago by rah20 • updated 8 weeks ago by Haci160
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Mapping quality in Oxford Nanopore
... Now i've seen in several post here at Biostars, that if we have mapping qualities of 0, this means the reads are multimapping. The data im analyzing comes from Oxford Nanopore sequencing which in general have a higher sequencing error, when compared to other sequencing tools. So my question woul ...
minimap2 mapping quality oxford nanopore written 3 months ago by rah20 • updated 8 weeks ago by Biostar ♦♦ 20
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Comment: C: Low Mapping percentage with Minimap2 due to contamination
... Thank you, ill give it a look ...
written 7 months ago by rah20
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Comment: C: Low Mapping percentage with Minimap2 due to contamination
... Thanks for suggesting to cut the reads into smaller pieces, because one of my problems has exactly been im having long reads. ...
written 7 months ago by rah20
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Low Mapping percentage with Minimap2 due to contamination
... Hi everyone, Im analysing Oxford Nanopore sequenced DNA in human cells, which i align to the hg19 UCSC reference genome. Most of the time i get a high mapping percentage, however in a few cases i get mapping percentages below 5%. Of course im able to tune the parameteres of minimap2 a bit, but i ...
minimap2 reference genome mapping nanopore written 7 months ago by rah20
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Comment: C: Extract several parts from fasta header
... It looks really useful. Thanks! ...
written 8 months ago by rah20
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Comment: C: Extract several parts from fasta header
... Thanks for your suggestions for both options. ...
written 8 months ago by rah20
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Comment: C: Extract several parts from fasta header
... Because i didn't think of that, all of the examples i could find handling fasta headers was using grep, so i thought i might as well stay with using grep. well that worked perfectly, thanks ...
written 8 months ago by rah20
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Extract several parts from fasta header
... I'm looking for a way to create an text file containing some information about sequence reads, extracted from a .fasta file. Either by using grep, sed or awk. Basically i have several fasta sequences which i have trimmed, so i an example of a header for a trimmed fasta file with a sequence where i ...
fasta grep sed unix bash written 8 months ago by rah20
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Comment: C: Bash: For loop with two statements, first statements as input to second with .fa
... Thanks for your respons, i'll give it a try when im doing my next round of analysis. ...
written 8 months ago by rah20

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