User: SOHAIL

gravatar for SOHAIL
SOHAIL310
Reputation:
310
Status:
Trusted
Location:
Beijing Institute of Genomics, CAS.
Last seen:
11 months, 2 weeks ago
Joined:
5 years, 2 months ago
Email:
m*****************@live.com

Posts by SOHAIL

<prev • 71 results • page 1 of 8 • next >
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Comment: C: Plotting F3 statistics values on world map
... @Jean-Karim, Thanks for your reply. is there any way to get the approximate Lat. and long. information, if the exact info. is unknown and haven't collected during sample collection, but the city/province/area names are known... ...
written 21 months ago by SOHAIL310
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Comment: C: Plotting F3 statistics values on world map
... Hi @zx8754, The example dataset includes many populations with F3-statistics values. For instance, F3(TARGET, X, OUTGROUPPOP), where the X pop with their corresponding output values are e.g.: X f3 Altaian 0.184 Dolgan 0.189 Ket 0.176 Karitiana 0.185 Hezhen 0.204 Daur 0. ...
written 21 months ago by SOHAIL310
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Plotting F3 statistics values on world map
... Hi Everybody, I calculated f3-statistics values with admixtools using combination (TARGETPOP, WORLD_WIDEPOPS, OUTGROUP), now i want to draw the data values for given population in terms of color circle points on world map. I started from here http://eriqande.github.io/rep-res-web/lectures/making-map ...
R ngs written 21 months ago by SOHAIL310
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Comment: C: reference genome hs37d5 with PhiX
... Thanks, @Kelso for the kind response. ...
written 21 months ago by SOHAIL310
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Select the transversions only from SNP data set
... Hi everybody, I wanna perform the F3-statistics and D-statistics on my data set, is there any way to select the transversions only from my snp call set, my data set is in plink bed/bim/fam file format.. thanks in advance! ...
ngs plink written 22 months ago by SOHAIL310
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Comment: C: reference genome hs37d5 with PhiX
... @genomax Hi, The illumina genome that you shared has the following info: From the "genome.dict" file of the illumina phiX genome: @SQ SN:phix LN:5386 UR:file:/illumina/scratch/iGenomes/PhiX/Illumina/RTA/Sequence/WholeGenomeFasta/genome.fa M5:bb9dae7b38a25a45dae8e3179d7c4241 Different than ...
written 24 months ago by SOHAIL310
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Comment: C: reference genome hs37d5 with PhiX
... @ Gabriel R, Thank you for the special favor... and yes, of course, I have gone through this URL before that you gave: http://cdna.eva.mpg.de/neandertal/Chagyrskaya/bam/README All the contig names and length information is in accordance with the BAM file that's given in the README except phiX leng ...
written 24 months ago by SOHAIL310
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Comment: C: reference genome hs37d5 with PhiX
... @ Gabriel R, yes! You are right. The BAM files are from Max Planck Inst. in Leipzig. can you share your ref, please...? ...
written 24 months ago by SOHAIL310
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reference genome hs37d5 with PhiX
... Hi everybody, can anyone guide me from where to download the hs37d5.fa genome merged with phiX genome? I have downloaded few BAM files containing the tag in header section @SQ SN:PhiX LN:6386 together with other hs37d5/fa contigs. I am looking for which version of the reference sequence was used ...
ngs reference genome written 24 months ago by SOHAIL310 • updated 21 months ago by kelso20
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Comment: C: Remove ambiguous calls in the VCF file
... @ATpoint, The lines with M (and others Y, R, W, K, S, (i.e. two-base ambiguity codes) ) in VCF file will be removed. edit: any help??? ...
written 24 months ago by SOHAIL310

Latest awards to SOHAIL

Appreciated 19 months ago, created a post with more than 5 votes. For Haplotype Phasing with Shapeit2
Great Question 19 months ago, created a question with more than 5,000 views. For VCF to BCF file conversion
Great Question 19 months ago, created a question with more than 5,000 views. For Generate Consensus sequence from BAM file
Great Question 19 months ago, created a question with more than 5,000 views. For BWA-MEM Vs BWA-ALN
Good Question 19 months ago, asked a question that was upvoted at least 5 times. For Haplotype Phasing with Shapeit2
Popular Question 19 months ago, created a question with more than 1,000 views. For flagstats results show 0.0 % properly paired reads
Popular Question 19 months ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Popular Question 19 months ago, created a question with more than 1,000 views. For tools for Population branch statistics (PBS)
Popular Question 19 months ago, created a question with more than 1,000 views. For How to combine variants??
Popular Question 19 months ago, created a question with more than 1,000 views. For Filtering no-calls from VCF file
Popular Question 19 months ago, created a question with more than 1,000 views. For Parallelizing SAMTOOLS: how to make my command run faster?
Popular Question 19 months ago, created a question with more than 1,000 views. For Calculate the genotype frequency
Popular Question 19 months ago, created a question with more than 1,000 views. For calculate Per variant Heterozygosity from VCF file
Popular Question 22 months ago, created a question with more than 1,000 views. For flagstats results show 0.0 % properly paired reads
Great Question 22 months ago, created a question with more than 5,000 views. For VCF to BCF file conversion
Popular Question 22 months ago, created a question with more than 1,000 views. For split reads for different lanes in BAM files
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Processing FASTQ files after fastq-dump
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How to get adapter information from SRA dump FASTQ file??
Popular Question 2.0 years ago, created a question with more than 1,000 views. For flagstats results show 0.0 % properly paired reads
Popular Question 2.1 years ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Processing FASTQ files after fastq-dump
Great Question 2.4 years ago, created a question with more than 5,000 views. For VCF to BCF file conversion
Student 2.4 years ago, asked a question with at least 3 up-votes. For Haplotype Phasing with Shapeit2
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Processing FASTQ files after fastq-dump
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Processing FASTQ files after fastq-dump

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