User: stolarek.ir

gravatar for stolarek.ir
stolarek.ir530
Reputation:
530
Status:
Trusted
Location:
Poland
Last seen:
1 day, 11 hours ago
Joined:
4 years, 4 months ago
Email:
s**********@gmail.com

about me

Posts by stolarek.ir

<prev • 115 results • page 1 of 12 • next >
0
votes
0
answers
181
views
0
answers
Comment: C: Illumina paired end read header difference- SPAdes bwa run ERROR
... download bbmap and use repair.sh from it like so: ./repair.sh in1=pair1.fastq in2=pair2.fastq out1=out_pair1.fastq out2=out_pair2.fastq outsingle=out_single.fastq ...
written 8 weeks ago by stolarek.ir530
0
votes
1
answer
176
views
1
answers
Comment: C: RNASeq lane effect
... there might be something off if you multiplex hardly, and the indexes used within the lane do not co-op with each other well ...
written 8 weeks ago by stolarek.ir530
0
votes
1
answer
244
views
1
answers
Comment: C: long reads Pacbio SNP calling
... either look at their webpage if they have anything dedicated for that, or use GATK ...
written 9 weeks ago by stolarek.ir530
1
vote
1
answer
244
views
1
answers
Answer: A: long reads Pacbio SNP calling
... no worries, with high coverage you can do a decent SNP calling using PacBio ...
written 9 weeks ago by stolarek.ir530
0
votes
0
answers
136
views
0
answers
codeml, output tree topology different from the input tree
... Dear all, I am struggling with understanding the output of the codeml. I used typical M0 model with settings like so: runmode = 0 seqtype = 1 CodonFreq = 2 clock = 0 model = 0 NSsites = 0 The provided tree (runmode = 0) is however severely altered in the o ...
paml codeml written 9 weeks ago by stolarek.ir530
2
votes
1
answer
485
views
1
answers
Comment: C: Paired vs unpaired (DNA Sequencing)
... cmon, at least use google and read about anything on the first page ...
written 3 months ago by stolarek.ir530
0
votes
0
answers
294
views
0
answers
Comment: C: How to align multiple genomic regions simultaneously
... I don't really get it. Is the problem that aligner takes one read and maps it? This is how it's done, alignment of each read is independent from other reads ...
written 3 months ago by stolarek.ir530
0
votes
1
answer
291
views
1
answers
Answer: A: PLINK RECODING ISSUE
... the way I do it is to first genotype the vcf files I have with a common set of SNPs (in other words genotype against a list of SNP positions, so that every individual genotyped is going to have the same number of markers). bedtools intersect -a my.vcf -b bed_present_snps -wa -header > out.v ...
written 3 months ago by stolarek.ir530
1
vote
0
answers
265
views
0
answers
Comment: C: Ancestry Informative Markers
... not really. If you have everything set up correctly (the genome versions are the same - thus, the positions of markers correspond between reference samples and your samples) you can even use plink to select only the markers that you want (by these I mean the markers from reference file). This is als ...
written 3 months ago by stolarek.ir530
2
votes
0
answers
265
views
0
answers
Comment: C: Ancestry Informative Markers
... You can always go and search google for AIMs, but that will give you a set of 20 or 200 markers, which are good for broad continental distinctions. A better approach could be to genotype against some big set of good markers, for example Human Origins set (about 600k markers) or markers derived from ...
written 3 months ago by stolarek.ir530

Latest awards to stolarek.ir

Great Question 13 days ago, created a question with more than 5,000 views. For Python Cigar String - Finding Indels Break Points Positions
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Genotype Likelihoods
Popular Question 4 months ago, created a question with more than 1,000 views. For plink 1.9 PED to VCF, SNPs differ on input and output files
Popular Question 6 months ago, created a question with more than 1,000 views. For Extract Regions Of Genome That Have 0 Coverage
Centurion 7 months ago, created 100 posts.
Popular Question 7 months ago, created a question with more than 1,000 views. For Extract Regions Of Genome That Have 0 Coverage
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Genotype Likelihoods
Popular Question 14 months ago, created a question with more than 1,000 views. For Extract Regions Of Genome That Have 0 Coverage
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Split Reads vs Supplementary Reads
Popular Question 21 months ago, created a question with more than 1,000 views. For Python Cigar String - Finding Indels Break Points Positions
Popular Question 23 months ago, created a question with more than 1,000 views. For Extract Regions Of Genome That Have 0 Coverage
Popular Question 23 months ago, created a question with more than 1,000 views. For Extract Regions Of Genome That Have 0 Coverage
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Python Cigar String - Finding Indels Break Points Positions
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Python - Scan Thorugh A Large File And Report Matches In Vcf File Under Conditions

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1020 users visited in the last hour