User: rah

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rah20
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Posts by rah

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Human contamination in Chimpanzee or Bonobo data
... Thanks for your reply, I'll check that out. Yes, I am aware that it's going to be difficult since they are closely related. Yes, i have sequence data for both Bonobo and Chimpanzees, another problem is then that the general read depth is below 5. Do you know any conceptual things i could try out to ...
written 6 weeks ago by rah20
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Human contamination in Chimpanzee or Bonobo data
... Im currently working with chimpanzee and Bonobo data, and i am curious to know if the datasets are contaminated with human DNA. I know that that a potential issue is that generally the chimpanzee reference genome and human genome are quite similar. And that the assembly PanPan3 reference genome is ...
next-gen alignment contamination sequencing written 6 weeks ago by rah20
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Comment: C: Combine multiple samtools view
... yeah sorry for the mistake, thats what i meant by filtering out. I want to remove all the reads with XA and SA tag. Afterwards i want to extract all the reads which aligns to chr 1-22, x,y,m ...
written 8 weeks ago by rah20
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Combine multiple samtools view
... Can anyone help me with combining two samtools view commands into a single command. I need to remove some alignment tags "XA and SA" and afterwards i also need to keep only the aligned reads to the "canonical" chromosomes from a reference genome. It is possible to do all of this in multiple steps ...
alignment samtools bam written 8 weeks ago by rah20 • updated 8 weeks ago by GenoMax96k
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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 4 months ago by rah20 • updated 4 months ago by Ram32k
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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 17 months ago by rah20 • updated 17 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 19 months ago by rah20 • updated 18 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 23 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 23 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 23 months ago by rah20

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