User: lait

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lait120
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Posts by lait

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Comment: C: find coverage of specific exomes from a bam file
... ASCII text and the second command returned nothing So in my case, the start and end coordinates are equal, I dont know why the condition turned to be TRUE ...
written 4 weeks ago by lait120
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Comment: C: find coverage of specific exomes from a bam file
... just figured out the error, the bed file contains locations of length = 1 (a single nucleotide). it should be of length 2 or more , because of the condition present in your java file. ...
written 4 weeks ago by lait120
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Comment: C: find coverage of specific exomes from a bam file
... when replacing chx with x , I get the message "ignoring" for all the entries in the bed file ...
written 4 weeks ago by lait120
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Comment: C: find coverage of specific exomes from a bam file
... Hi Pierre, why do I always get the error: Unknown contig ? which refers to the first line in my bed file ? I tried to play around with the bed file , use different coordinates, but I always get this error. My bed file is something similar to: ch1 115256528 115256530 ch2 ....... ...
written 4 weeks ago by lait120
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Comment: C: find coverage of specific exomes from a bam file
... thanks for sharing! ...
written 4 weeks ago by lait120
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Comment: C: find coverage of specific exomes from a bam file
... thanks! do you have an idea how to solve this error when installing Alfred: sudo conda install -c bioconda alfred Fetching package metadata ............. PackageNotFoundError: Package not found: '' Package missing in current osx-64 channels: - alfred ...
written 4 weeks ago by lait120
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find coverage of specific exomes from a bam file
... Hi I know that bedtools genomecov -ibam xx.bam -bg would report genome coverage in BEDGRAPH format What if I need the coverage not for the whole genome, but just for specific regions (specific exomes) ? how can I achieve this ? my input files are a bam file and a .bed file containing the ...
bedtools genomecov bam coverage bed written 4 weeks ago by lait120 • updated 4 weeks ago by Pierre Lindenbaum115k
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Comment: C: Course: Practical GWAS using Linux and R. 23-27 October 2017, Berlin (Germany)
... is it fully booked? any chance to register? Edit: just released I am 1 year late ...
written 8 weeks ago by lait120
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snps/indels with individual genotypes from 1000 genomes ftp site
... Sorry if this might be a trivial question! I read a lot about this until I got lost. I need to download wgs VCF file from the 1000 genomes ftp site. I need the snps (snvs and indels), most importantly, I need to have the individual genotypes of all the persons involved. so for example, this file : ...
vcf 1000 genomes genotypes ftp written 3 months ago by lait120 • updated 3 months ago by Kevin Blighe33k
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most efficient way to read from large vcf files
... Hi, if I have a large VCF file (for example, from the 1000 genomes project), what could be the most 'efficient' way (R libraries?) to extract variants from this file that lie in certain genomic regions ? The way I used to do it with small vcf files is to load them in memory and start digging, but ...
vcf written 3 months ago by lait120

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