User: dschika

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dschika300
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European Union
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1 year, 10 months ago
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Posts by dschika

<prev • 51 results • page 1 of 6 • next >
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Comment: C: I get almost the same fastqc report for a fastq file before and after using Trim
... The result of the trimming looks ok for me. The quality of your data set is not the best. Removing adaptors and trimming low quality ends from reads (-q) leads to an increase in the overall mean quality values towards the end, which is visible in after.png. Given the before.png result, I would not ...
written 2.1 years ago by dschika300
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Comment: C: Valid or invalid vcf? REF nucleotide is not matching reference in vcf lines wher
... Thanks, Pierre. I am still not sure if I understood the manual: It menas, that in such CNV-lines POS equals REF allele - 1? ...
written 2.6 years ago by dschika300
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Comment: C: Valid or invalid vcf? REF nucleotide is not matching reference in vcf lines wher
... Yes. Here is an example line: chr1 11174372 . A 100.0 PASS FR=.;PRECISE=FALSE;SVTYPE=CNV;END=11217311;LEN=42939;NUMTILES=7;SD=0.21;REF_CN=2;CI=0.05:1.60885,0.95:2.43413;RAW_CN=1.99 GT:GQ:CN ./.:0:1.99 Nucleotide at position 11174372 on chr1 is C. Nucleotide at position 11174373 on chr1 is A. ...
written 2.6 years ago by dschika300
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Valid or invalid vcf? REF nucleotide is not matching reference in vcf lines where ALT equals <CNV>
... Hi, I got a vcf file and the first I checked was if the first nucleotide given at REF matches the nucleotide in the reference at position POS. This was true for lines with SNPs, indels, and breakends, but not for lines having "< CNV>" as ALT. In those < CNV>-lines the REF nucleotide alw ...
vcf cnv written 2.6 years ago by dschika300 • updated 2.6 years ago by Pierre Lindenbaum129k
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Comment: C: Error: --fst requires at least two nonempty clusters.
... I have to admit that I have not used plink with --fst before. Therefore, this is just a guess from the error message: Is it possible that you did not define a second cluster in IDsparahw.txt file except of EUR ? ...
written 3.1 years ago by dschika300
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Comment: C: Grep Position List
... Well, "chr1" is not equal "1" ... ...
written 3.1 years ago by dschika300
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Comment: C: Grep Position List
... Hm...could you please double check: How does Chr.pos.tsv look like? Have you included chromosomes? Are chromosome and position tab-separated? How does myNew.vcf look like? Is there more than just the header-section? Are there chromosome-position pairs matching your Chr.pos.tsv file? ...
written 3.1 years ago by dschika300
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Comment: C: Grep Position List
... Try adding: --recode ...
written 3.1 years ago by dschika300
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Comment: C: Grep Position List
... Have you tried [vcf-compare][1] from vcftools? [1]: https://vcftools.github.io/perl_module.html#vcf-compare ...
written 3.1 years ago by dschika300
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Answer: A: Grep Position List
... What about [vcftools][1]: > --positions > > Include or exclude a set of sites on the basis of a list of positions > in a file. Each line of the input file should contain a > (tab-separated) chromosome and position. The file can have comment > lines that start with a "#", they will ...
written 3.1 years ago by dschika300

Latest awards to dschika

Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: getting error i don't understand using biopython for retrieving sequences from f
Scholar 4.3 years ago, created an answer that has been accepted. For A: getting error i don't understand using biopython for retrieving sequences from f
Scholar 4.5 years ago, created an answer that has been accepted. For A: How to export FDR info when exporting loci list in LOSITAN
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: getting error i don't understand using biopython for retrieving sequences from f
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: getting error i don't understand using biopython for retrieving sequences from f
Scholar 4.6 years ago, created an answer that has been accepted. For A: How to export FDR info when exporting loci list in LOSITAN
Scholar 4.6 years ago, created an answer that has been accepted. For A: How to export FDR info when exporting loci list in LOSITAN

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