Moderator: finswimmer

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finswimmer8.9k
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Posts by finswimmer

<prev • 1,244 results • page 2 of 125 • next >
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Answer: C: What is the best way to get all human genes(name/UID) ?
... You can use [Biomart][1] to get all gene names. You may want to choose `Limit to genes (external references)... ` `With RefSeq mRNA ID(s)` in the `Filter` tab. fin swimmer [1]: http://www.ensembl.org/biomart/martview/ ...
written 1 day ago by finswimmer8.9k
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Comment: C: bedtools, merge function: avoid merging intervals if separated by a single base
... Hello https://www.biostars.org/u/39894/ , the output of `bedtools` is interesting. I'm not sure whether this a bug or by design. Nevertheless I think your `bed` doesn't represent the positions you think. `bed` uses 0-based, half open intervals. That means it starts counting the position with 0 in ...
written 2 days ago by finswimmer8.9k
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Comment: C: SO:coordinate Error parsing text SAM file. Line: BAM#Pm@HD VN:1.5 SO:coordinate
... Hello https://www.biostars.org/u/43441/ , could you please show us all commands, that were used to generate your `bam` file? The first lines of the bam file must begin with a `@`, because this introduce the header information. A `#` is just as false as a "small binary number-looking symbol contai ...
written 3 days ago by finswimmer8.9k
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Comment: C: Randomly select one variant from heterozygous sites in VCF file
... Hello, could you please provide an example of your desired output? fin swimmer ...
written 4 days ago by finswimmer8.9k
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Answer: A: Create multiple files using awk
... There is a variable called `FILENAME` which provide the current filename `awk` reads in. You can take this to create a filename `awk` should print its output. $ awk 'NR==FNR{vals[$1];next} ($1) in vals { print $0 >> "new_"FILENAME}' indiv.txt file1.txt file2.txt file3.txt fin swimmer ...
written 6 days ago by finswimmer8.9k
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Answer: A: how to find the overlapping genomic sites for two big mpileup files and make a w
... Also this is a quite old question, maybe you or other are interested in a possible way. First let's create a bed file, containing intervals of covered site in each mpileup file. As this question is 10 month old, I assume you have the output of `samtools mpileup` where the first column contains the ...
written 6 days ago by finswimmer8.9k
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Comment: C: vcf tools (vcf-stats) not able to generate stats ?
... If you just want the total number of SNPs and INDEL, there are many ways. But first check if there are multiple header blocks. Working with a corrupted file will always lead to problems sooner or later. fin swimmer ...
written 6 days ago by finswimmer8.9k
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Comment: C: Brief Reminder On How To Ask A Good Question
... Thanks for this https://www.biostars.org/u/25721/ . In addition: [Ten Simple Rules for Getting Help from Online Scientific Communities][1] Also if you find the solution for your problem by yourself, please be so kind to report this. Other users may have the same problem and will be very glad to fi ...
written 6 days ago by finswimmer8.9k
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Answer: A: Pysam VariantFile.fetch() without specifying contig
... Hello, you can get all the contig names via `VCF.header.contigs`. This returns a view you can iterate over (untested): for name in VCF.header.contigs: VF.fetch(contig=name, start=0, end=1000) This presumes that the contigs are listed in the header. fin swimmer ...
written 6 days ago by finswimmer8.9k
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Comment: C: vcf tools (vcf-stats) not able to generate stats ?
... What kind of stats to you expect? Nevertheless you should investigate the error message: Multiple header blocks (^#) not allowed. Run `grep -n "^#" 15Mar11_R1_dedup_2_ReadGroups.bam_GATK.vcf` This will give you all lines, that start with a `#` and add the line number at the beginning. These n ...
written 6 days ago by finswimmer8.9k

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