User: rjobmc

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rjobmc0
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Posts by rjobmc

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Comment: C: Relatedness software for 20,000 exome sequencing datasets.
... Hi Shicheng Guo, Where can I get these tag-SNPs for both WES and WGS? I presume it would be based on LD scores < 0.2 or something like that? Thanks for your help. ...
written 4 months ago by rjobmc0
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Relatedness software for 20,000 exome sequencing datasets.
... Hi all, I have a dataset of around 20,000 exomes and I need a quick and efficient tool to look for relatedness in all of my samples. I have tried "relatedness2" from vcftools but it is very slow. It's also "pair-wise" and so not very efficient. We use we use multi-vcf.gz files. Does anyone know of ...
vcf relatedness vcf.gz written 4 months ago by rjobmc0 • updated 4 months ago by Shicheng Guo7.4k
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Comment: C: Extract start coordinate from read 1 and end coordinate from read 2 of paired en
... I checked > btw, cross check if this holds true if your r1 is on - instead of + And it worked perfectly. > BTW, what would happen to multi mapping reads? This was just an example but your command has worked perfectly for all reads (multi and unique). Thanks again :) ...
written 6 months ago by rjobmc0
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Comment: C: Extract start coordinate from read 1 and end coordinate from read 2 of paired en
... $ sed 's/\/.*//g' test.txt | datamash -sg 1,4 min 2 max 3 | cut -f1,3,4 Worked perfectly! Thanks so much. ...
written 6 months ago by rjobmc0
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Comment: C: Extract start coordinate from read 1 and end coordinate from read 2 of paired en
... `$ awk -v OFS="\t" '$4 ~ "/1" {print $1,$2,$3}' test.txt` Unfortunately this didnt work, it just pulls out the end coordinate of read 1, when I need the read 2 end coordinate ...
written 6 months ago by rjobmc0
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Comment: C: Extract start coordinate from read 1 and end coordinate from read 2 of paired en
... $ sort -k4,4 inputfile|paste - -|cut -f1,2,9 > outputfile Thanks fin swimmer, but it has not worked. The reads are sorted by reads and not chr, start, end and so they are not in numerical/chromosomal order. Is there any way to check that the read pair "code" is the same, ie its the /2 of th ...
written 6 months ago by rjobmc0
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Comment: C: Extract start coordinate from read 1 and end coordinate from read 2 of paired en
... cut -d' ' -f1-3 inputfile > outputfile This did not work ...
written 6 months ago by rjobmc0 • updated 6 months ago by finswimmer11k
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Extract start coordinate from read 1 and end coordinate from read 2 of paired end reads.
... Hi there. Im looking to extract chr, start coordinate of read 1 and the end coordinate of read 2 of paired-end NGS into one "bed" file. I have over 7 million reads and I am not sure that every paired-end read has a "pair". I have used bamtobed function of bedtools and sorted the file by read info (e ...
bedtools unix written 6 months ago by rjobmc0 • updated 6 months ago by finswimmer11k
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Comment: A: Adding legend to word cloud
... As a follow up to my question, the R code I am using is the following: R Package: Wordcloud Code: > wordcloud(d$word, d$freq, random.order=F, colors=(colorRampPalette(brewer.pal(9,"Blues"))(30)), scale=c(4, .4)) File "d" = filename word = GO term Freq = Fold enrichment This allows me to make ...
written 18 months ago by rjobmc0
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Comment: C: Adding legend to word cloud
... Yes it is. Thanks for the suggestion. ...
written 18 months ago by rjobmc0

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Popular Question 15 months ago, created a question with more than 1,000 views. For Standard Deviation using log2 values

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