User: ahmedakhokhar

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ahmedakhokhar110
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Posts by ahmedakhokhar

<prev • 48 results • page 1 of 5 • next >
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Comment: C: locating positions of a Fasta seq in bam file
... samtools view [options] in.sam|in.bam|in.cram [region...] samtools view; takes [region] coordinates, which I don't have for this seq. This is the problem I am facing. any tips? ...
written 7 days ago by ahmedakhokhar110
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Comment: C: locating positions of a Fasta seq in bam file
... Yes, the bam file was generated from the usual genome sequencing pipeline and it should contain this .fasta seq too. I just want to know where .fasta seq present in the aligned sequence. (genomic coordinates of my .fasta seq in the bam alignment file) ...
written 7 days ago by ahmedakhokhar110
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locating positions of a Fasta seq in bam file
... Hi, I am new to whole-genome alignments and sequencing (and this naive question might have asked before and answer several times, my humble apologies). I have a sequence in a .fasta file (length ~3kb) without its genomic coordinates; all I want to know is that: what is the genomic location of this ...
assembly written 8 days ago by ahmedakhokhar110
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Comment: C: SNP Analysis on Single Cell Data from 10x
... Try to check it out! https://www.scrna-tools.org ...
written 9 months ago by ahmedakhokhar110
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Comment: C: print lines with specific members only
... Done, thank you ...
written 9 months ago by ahmedakhokhar110
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Comment: C: print lines with specific members only
... Thanks, I am new to 'awk', can you please give an example how can I match "p1'" and "w3" from a line and print? Thank you so very much. ...
written 9 months ago by ahmedakhokhar110
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Comment: C: print lines with specific members only
... I am working with "Bioinformatics" data, the p1, w3 are different cell types. ...
written 9 months ago by ahmedakhokhar110
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(Closed) print lines with specific members only
... I have a dataset with following format: a. 1 w p1,p2,w3 b. 1 w p1,p2,p3, w3 c. 1 w p1,w3 d. 1 w p1,w3 I want to print only the lines where 'p1,w3' present but not any of lines where p1, w3 are present in combination with other members like p1,p2,w3 ... c. ...
python R written 9 months ago by ahmedakhokhar110
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Comment: C: group samples based on shared mutations in a single multi samples vcf file
... Perfect, that can work nicely, one more piece of help. The sample names start with either "A_" or "B_" (followed by individual names). How can I count the sub-population of samples? Thank you very much. ...
written 10 months ago by ahmedakhokhar110
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Comment: C: group samples based on shared mutations in a single multi samples vcf file
... samples with 0/1 and 1/1 for the same positions with go as a separate entry but if I can get info of 1/1 only, that would be sufficient. The final aim is to know which samples share which mutation (position) and to separate them into groups. ...
written 10 months ago by ahmedakhokhar110

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Great Question 6 months ago, created a question with more than 5,000 views. For read contents of a file from a list of file with os.listdir() (python)
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Epic Question 8 months ago, created a question with more than 10,000 views. For read contents of a file from a list of file with os.listdir() (python)
Great Question 9 months ago, created a question with more than 5,000 views. For read contents of a file from a list of file with os.listdir() (python)
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