User: waqaskhokhar999

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Posts by waqaskhokhar999

<prev • 85 results • page 1 of 9 • next >
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Comment: C: Plot GWAS p value distribution for multiple traits
... I have manhattan plots for each trait but is there any way by which I can plot manhattan plot for all traits together to see the p-value distribution ...
written 3 months ago by waqaskhokhar999100
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Comment: C: Plot GWAS p value distribution for multiple traits
... I have ploted the qq plot for all traits together but it depeicts expected vs actual p-values and the graph is not very much clear that's why i am trying to look for other options ...
written 3 months ago by waqaskhokhar999100
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Plot GWAS p value distribution for multiple traits
... I have 10,000 SNPs and 48 different phenotypic traits, so I performed GWAS based on Mixed Linear Model (MLM) approach using Tassel. I have got associations and now I am interested to see the distribution of p values to better [interpret p-values][1] so I extracted the p-values for all traits from t ...
plotting gwas R written 3 months ago by waqaskhokhar999100
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Indentify character and keep corressponding character from bottom two rows
... I have a large tab-delimited file and a part of it is like: 25 M X A A X S 25_a M K A A R S 25_b M A A A V S 31 M A A A V S 31_a M A A A V S 31_b M A A A V S I am trying to play with three rows at a time, the first row contains a reference sequence (actual sequence ...
rna-seq written 9 months ago by waqaskhokhar999100 • updated 9 months ago by JC12k
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Combine fasta files by matching partial header in specific format
... I have three fasta files reflecting protein sequences for each gene in xls format (space separated). The first column contains header, while the other column contains sequence. For example: File1: sample 1 2 3 4 5 6 BnaA03g18710D M A A A V S BnaA03g18710D_S25 M A A A V S BnaA03g187 ...
rna-seq written 10 months ago by waqaskhokhar999100
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Comment: C: Replace ambigious nucleotide with correct nucleotides
... Many thanks for this guidance, I have tried to work on regex but didn't get success, So I thought instead of finding the nucleotide sequence for ambiguous codon, I can start with CDS sequence that is coding for those codons and can sort out the ambiguous nucleotide. I understand the first point but ...
written 10 months ago by waqaskhokhar999100
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Replace ambigious nucleotide with correct nucleotides
... I have multi fasta nucleotide file, I am interested to replace the [ambigious nucleotides][1] (R, Y, S, K, e.t.c) with a possible combination of nucleotides and save both options. For example, the following nucleotide sequence (sudo example): >Seq1 ATGGKCRCCGCSGT Contain ambiguous nucle ...
next-gen rna-seq written 10 months ago by waqaskhokhar999100 • updated 10 months ago by _r_am32k
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Comment: C: Replace Ambigious codons with Amino acid sequences
... I would like to keep both combinations, in the sequence a the yag will become cag and codes for Q, while in the sequence b the yag will become tag and reflects stop codon (*) and the outputs would be like these: >ORF1_BnaA03g18710D_S45:82:1509_a MAAAVSTVGAINRAPLSLNGSGAGAASVPATTFLGKKVVTAS ...
written 10 months ago by waqaskhokhar999100 • updated 10 months ago by _r_am32k
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Replace Ambigious codons with Amino acid sequences
... I have two multi-fasta files, one contains nucleotide sequences, and a subset of nucleotide sequence for ORF1 is: >ORF1_BnaA03g18710D_S45:82:1509 ATGGCCGCCGCAGTTTCCACCGTCGGTGCCATCAACAGAGCTCCGTTGAGCTTGAACGGG TCAGGAGCAGGAGCTGCTTCAGTCCCAGCTACGACCTTCTTGGGAAAGAAAGTTGTAACC GCGTCGAGATTC ...
sequence rna-seq written 10 months ago by waqaskhokhar999100 • updated 10 months ago by Asaf8.5k
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Comment: C: How to extract the longest orf?
... Can you please tell me how I can use get_longest_ORF_per_transcript.pl script, I have tried following command: perl TransDecoder-TransDecoder-v5.5.0/util/get_longest_ORF_per_transcript.pl input_file But got this error: Error, cannot parse header info: BnaA03g18710D_ref at TransDecoder-TransDeco ...
written 10 months ago by waqaskhokhar999100

Latest awards to waqaskhokhar999

Popular Question 9 months ago, created a question with more than 1,000 views. For Alternative splicing events in transcriptomic data
Popular Question 9 months ago, created a question with more than 1,000 views. For strandness of paired-end data
Supporter 11 months ago, voted at least 25 times.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Alternative splicing events in transcriptomic data

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