Moderator: finswimmer

gravatar for finswimmer
finswimmer11k
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Germany
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2 years, 1 month ago
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Posts by finswimmer

<prev • 1,423 results • page 2 of 143 • next >
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Comment: C: I have a list of chromosomes, positions, gene ids, and transcript ids (from a ge
... Hello again, it is still not clear what you are trying to do and **why**. Please descibe this to get proper help. Thanks! fin swimmer ...
written 16 days ago by finswimmer11k
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Comment: C: I have a list of chromosomes, positions, gene ids, and transcript ids (from a ge
... Hello https://www.biostars.org/u/45050/ , could you please explain why you like to do this? GTF have no information about REF and ALT. It just describes a certain feature (in your case "exon") in a given region. fin swimmer ...
written 21 days ago by finswimmer11k
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Answer: A: How to consider/get the g. positions for variants in introns?
... Hello, ensembl's [VEP][1] can do this. Along with the `c.` you have to provide a gene id, gene name or Transcript id. In case you not use a transcript id, be aware that the result can be ambiguous.. fin swimmer [1]: http://www.ensembl.org/Homo_sapiens/Tools/VEP ...
written 21 days ago by finswimmer11k
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Comment: C: Bcftools Call method not detecting single nucleotide deletions?
... Hello https://www.biostars.org/u/53837/ , what are the values for `"$1"` and `"$2"`? fin swimmer ...
written 22 days ago by finswimmer11k
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Comment: C: Approximately following the GATK recommended workflow for DNA sequence data, my
... How was the library done? Is this amplicon based? I'm asking because you have a very high duplication rate and in case of amplicon based data, you cannot mark duplicates. ...
written 22 days ago by finswimmer11k
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Comment: C: Subsampling one bamfile multiple times?
... Hello https://www.biostars.org/u/53795/ , it is still unclear what's your problem. Just run the subsampling command multiple times with different parameters and your are done, aren't you? Or which point I'm missing? fin swimmer ...
written 23 days ago by finswimmer11k
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Answer: A: Should I use the same reference indexing command of bwa for WGS and WES analysis
... Hello, `-a bwtsw` describes the algorithm used for constructing the Burrow-Wheeler-Tree of the reference genome. `bwa` uses different ones for "short" and "long" genomes (Where ever the border is ...). So this is independent of the analysis you are planning. If you just omit the `-a` parameter `bw ...
written 23 days ago by finswimmer11k
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Comment: C: VCF INFO AC field for failed snps
... Hello https://www.biostars.org/u/34497/ , what you are showing is not valid vcf file. So the question is, do you have a valid vcf file (than show us) or does your file looks like you are showing here? fin swimmer ...
written 24 days ago by finswimmer11k
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Comment: C: How to edit fasta header with underscores
... Thank for providing the detailed examples. This is not a trivial task, because there is no clean pattern for the names you like to keep. > For some reason, a previous analysis adds the name of the species to the original sequences headers. So you have a file with "original sequence headers"? Ho ...
written 26 days ago by finswimmer11k
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Answer: A: The confused result of samtools sort
... Hello, `samtools sort` sort the reads by position for each contig. It doesn't sort the contig itself, because this is usually not necessary. The order of the contig names you see, is given by the order of the contigs in the reference file you specify during alignment. fin swimmer ...
written 27 days ago by finswimmer11k

Latest awards to finswimmer

Scholar 27 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: Filter Fastq file by seq
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For A: sam file error
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For A: sam file error
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Scholar 8 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
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Scholar 8 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
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