User: rah

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rah20
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Posts by rah

<prev • 15 results • page 1 of 2 • next >
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Htslib c++ library faidx fetch region
... I'm coding in c++ and reading in different reference genomes to examine regions across the chromosomes a few hundred base pairs at a time. To do it in c++ I use the library htslib and the command `faidx_fetch_seq()` which is similar to read specific regions using `samtools faidx`. The problem is w ...
htslib faidx samtools c++ written 28 days ago by rah20 • updated 28 days ago by _r_am30k
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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 14 months ago by rah20 • updated 14 months ago by Haci370
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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 16 months ago by rah20 • updated 14 months 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 20 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 20 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 20 months ago by rah20
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Comment: C: Extract several parts from fasta header
... It looks really useful. Thanks! ...
written 21 months ago by rah20
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Comment: C: Extract several parts from fasta header
... Thanks for your suggestions for both options. ...
written 21 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 21 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 21 months ago by rah20

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