Moderator: finswimmer

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finswimmer10k
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Posts by finswimmer

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Comment: C: help with python homework assignments
... Hello https://www.biostars.org/u/52730/ , please use the `ADD REPLY`button below the post you like to reply to. > I have Written my code but i don’t get the right results. Then show us the code, the result and your expected result. > i have a lot of silly questions Then ask your question! ...
written 4 hours ago by finswimmer10k
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Comment: C: Remove duplicate readnames from a bam file
... Hello https://www.biostars.org/u/52753/ , have you tried the things mentioned in https://www.biostars.org/p/60263/ ? Or here: https://gatkforums.broadinstitute.org/gatk/discussion/10115/picard-markdup-error-value-was-put-into-pairinfomap-more-than-once fin swimmer ...
written 4 hours ago by finswimmer10k
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Comment: C: Genomics (DNA) Pipeline - Example
... Yes, you need to create an index for the reference genome. How you create this index, depends on the aligner you like to use. E.g. for `bwa` it's a simple `bwa index genome.fa` ...
written 11 hours ago by finswimmer10k
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Comment: C: Incorrect number of AD fields (2) at 1:878906 cannot merge
... Hello https://www.biostars.org/u/52220/ , what version of `bcftools` are you using? Are you sure that `bcftools merge` is the right tool for your purpose? This tools merges vcf file from different samples to one multisample vcf . You have the same sample names in the different files. This should ...
written 12 hours ago by finswimmer10k
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Comment: C: How to check the presence of mutations of a specific gene in a specific VCF file
... Oops, sorry my fault. I edited my answer a bit. ...
written 13 hours ago by finswimmer10k
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Comment: C: Where to Download Cancer Raw Reads (fastq)?
... Hello https://www.biostars.org/u/50221/ , please tell us when you cross-post your question. This question is also asked on [stackexchange][1]. Thanks! fin swimmer [1]: https://bioinformatics.stackexchange.com/questions/7080/where-to-download-cancer-raw-reads-fastq ...
written 22 hours ago by finswimmer10k
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Answer: A: How to check the presence of mutations of a specific gene in a specific VCF file
... Hello https://www.biostars.org/u/3592/ , whether a simple `grep` for the gene name works, depends on if the vcf file is annotated with this information. The best way is to find chromosomal position of your gene of interest (for [ARIH1][1] this is 15: 72,474,326-72,602,985 in case you are using GRCh ...
written 22 hours ago by finswimmer10k
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Comment: C: bedtools intersect error?
... OK, let's do some more awk-voodoo. The following code will check for if there are white-spaces in the sequence name and if the start and end position contain only numbers. Those lines that are not valid will be written to `bad.bed`. All others go to `good.bed`, will be sorted and duplicates get r ...
written 23 hours ago by finswimmer10k
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Comment: C: bedtools intersect error?
... [This explanation][1] makes it more clear what's going on here. Your `bed` files are malformed. There are lines where the second or third column doesn't contain valid coordinates. This will give you the lines where the second or third column doesn't consist of one ore more numbers: $ awk -v FS ...
written 1 day ago by finswimmer10k
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Comment: C: bedtools intersect error?
... According to this [post][1], this error appears if you have duplicate entries in one of your file. Sort your files again after you have remove the white-spaces, but this time use `-u` to remove duplicates: $ sort -u -k1,1 -k2,2n input > output [1]: http://seqanswers.com/forums/showthread ...
written 1 day ago by finswimmer10k

Latest awards to finswimmer

Commentator 21 hours ago, created a comment with at least 3 up-votes. For A: sam file error
Cylon 1 day ago, received 1,000 up votes.
Scholar 2 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Appreciated 2 days ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Commentator 3 days ago, created a comment with at least 3 up-votes. For A: sam file error
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Popular Question 4 days ago, created a question with more than 1,000 views. For tabix for ID column
Scholar 5 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 14 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Prophet 15 days ago, created a post with more than 20 followers. For Creating workflows with snakemake and conda
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 16 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 16 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Popular Question 21 days ago, created a question with more than 1,000 views. For Creating workflows with snakemake and conda
Good Answer 21 days ago, created an answer that was upvoted at least 5 times. For A: what is the difference between polymorphism and mutation and variant?
Appreciated 22 days ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 24 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 4 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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