User: SOHAIL

gravatar for SOHAIL
SOHAIL80
Reputation:
80
Status:
Trusted
Location:
Beijing Institute of Genomics, CAS.
Last seen:
3 days, 20 hours ago
Joined:
1 year, 10 months ago
Email:
m*****************@live.com

Posts by SOHAIL

<prev • 48 results • page 1 of 5 • next >
0
votes
0
answers
103
views
0
answers
PSMC analysis: input data processing, mutation rate, generation time
... Hi Everybody, I have few questions regarding PSMC analysis, can anyone please guide me.. 1. What are the general masking filters that would be applied during input files processing in PSMC analysis for reliable results, and how to apply them? 2. During plotting PSMC plot construction, how to deci ...
psmc written 9 weeks ago by SOHAIL80
0
votes
3
answers
327
views
3
answers
Comment: C: Generate Consensus sequence from BAM file
... Hi @Dan, thanks for the answer.. can you suggest any way to run samtools faster? ...
written 3 months ago by SOHAIL80
0
votes
3
answers
327
views
3
answers
Answer: A: Generate Consensus sequence from BAM file
... Hi, I had a problem in running samtools/bcftools while generating consensus sequence. my command line was: samtools mpileup -C50 -uf REF.fa BQSR_AAGC0220.bam | bcftools view -c - | perl vcfutils.pl vcf2fq -d 8 -D 100 | gzip > AAGC0220.fq.gz later as i learnt bcftools modified the options f ...
written 3 months ago by SOHAIL80
0
votes
3
answers
327
views
3
answers
Comment: C: Generate Consensus sequence from BAM file
... Hi @Shengweima thanks for the help.. it works on small dataset.. can you please give an idea how much time it takes normally for 30X genome.? i am running my job from last 20 hours.. ...
written 3 months ago by SOHAIL80
3
votes
3
answers
327
views
3
answers
Generate Consensus sequence from BAM file
... Hi everyone, I want to generate diploid consensus sequence for one human individual from BAM file for PSMC analysis purposes. my command line is: samtools mpileup -C50 -uf REF.fa BQSR_AAGC0220.bam | bcftools view -c - | perl vcfutils.pl vcf2fq -d 8 -D 100 | gzip > AAGC0220.fq.gz The command ru ...
psmc samtools mpileup written 3 months ago by SOHAIL80
0
votes
2
answers
338
views
2
answers
Plotting Venn diagram for multiple BED files
... Hi Everyone, I have 6 large BED files and i want to draw a Venn diagram for them together. Can anyone please suggest which tool can handle multiple BED files simultaneously?? I have read about pybedtools https://daler.github.io/pybedtools/index.html But it handles only three files.. Can anyone pl ...
ngs venn diagram written 3 months ago by SOHAIL80 • updated 3 months ago by reza.jabal230
1
vote
1
answer
251
views
1
answers
Comment: C: comparing coordinates between two files
... I solved this partially by myself using bedtools... bedtools intersect -a file1.bed -b file2.bed -u > output.txt ...
written 3 months ago by SOHAIL80
2
votes
1
answer
251
views
1
answer
comparing coordinates between two files
... Hi, I have two files with content: File1 1 32030000 32080000 0.294180714 -1.124178317 1 32810000 32860000 -0.011122006 -0.508257648 2 32110000 32160000 -0.011122006 -0.613642043 File2: 1 32037085 32058287 NM_022164 1 32219260 32229336 NR_036216 2 32187705 32234664 NM_0 ...
ngs linux written 3 months ago by SOHAIL80 • updated 3 months ago by Alex Reynolds19k
0
votes
1
answer
354
views
1
answers
Comment: C: P-Value calculation from iHS and XP-EHH scores
... Hi @JM88, Thanks for your response, However, here in the comments you mentioned: "For iHS you can use the absolute standardised iHS scores. For XP-EHH -because this test is directional-, you should only use positive values." "Another option which is to compute approximate P-values by simulating t ...
written 4 months ago by SOHAIL80
5
votes
1
answer
354
views
6 follow
1
answer
P-Value calculation from iHS and XP-EHH scores
... Hi Everyone, I am anew in this. So forgive me if anything asking stupid! I calculated genome-wide standardized iHS and XP-EHH scores from 'Selscan' software. They both are present in negative and positive values. i read in some papers people choose |iHS| > 2 as a significant region cut-off, but ...
R selscan statistics ngs selection written 4 months ago by SOHAIL80 • updated 4 months ago by JM88270

Latest awards to SOHAIL

Popular Question 26 days ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Supporter 10 weeks ago, voted at least 25 times.
Student 4 months ago, asked a question with at least 3 up-votes. For P-Value calculation from iHS and XP-EHH scores
Popular Question 4 months ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Popular Question 22 months ago, created a question with more than 1,000 views. For VCF to BCF file conversion

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 429 users visited in the last hour