User: rjobmc

gravatar for rjobmc
rjobmc0
Reputation:
0
Status:
New User
Last seen:
3 months ago
Joined:
2 years, 10 months ago
Email:
r*****@ibmb.csic.es

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by rjobmc

<prev • 19 results • page 1 of 2 • next >
0
votes
1
answer
152
views
1
answers
Comment: C: Retrieve base count information for bases that are not variants
... In the end I used samtool depth a1.bed f1.bam, f2.ba etc.... a1.bed is a bed file with my positions. This worked perfectly! Thank you very much for your help. ...
written 7 months ago by rjobmc0
0
votes
1
answer
152
views
1
answers
Comment: C: Retrieve base count information for bases that are not variants
... Will this provide a read depth for every base in my bam file? ...
written 7 months ago by rjobmc0
3
votes
1
answer
152
views
1
answer
Retrieve base count information for bases that are not variants
... I am analysing RNA-seq data and I require read/allele depth information for a particular base position (I need this information for about 50 positions scattered around the genome in 8 individuals). As variant callers only give read depth information for variants, most of the positions I need are not ...
rna-seq base read depth written 7 months ago by rjobmc0 • updated 7 months ago by Pierre Lindenbaum124k
0
votes
1
answer
354
views
1
answers
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 12 months ago by rjobmc0
3
votes
1
answer
354
views
1
answer
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 12 months ago by rjobmc0 • updated 12 months ago by Shicheng Guo7.8k
0
votes
5
answers
681
views
5
answers
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 15 months ago by rjobmc0
0
votes
5
answers
681
views
5
answers
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 15 months ago by rjobmc0
0
votes
5
answers
681
views
5
answers
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 15 months ago by rjobmc0
0
votes
5
answers
681
views
5
answers
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 15 months ago by rjobmc0
0
votes
5
answers
681
views
5
answers
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 15 months ago by rjobmc0 • updated 15 months ago by finswimmer13k

Latest awards to rjobmc

Popular Question 6 months ago, created a question with more than 1,000 views. For Adding legend to word cloud
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Standard Deviation using log2 values

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1100 users visited in the last hour