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User: waqaskhokhar999

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Posts by waqaskhokhar999

<prev • 81 results • page 1 of 9 • next >
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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 2 days ago by waqaskhokhar999 • 80
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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 3 days ago by waqaskhokhar999 • 80
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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 3 days ago by waqaskhokhar999 • 80 • updated 3 days ago by RamRS ♦ 26k
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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 5 days ago by waqaskhokhar999 • 80 • updated 5 days ago by RamRS ♦ 26k
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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 5 days ago by waqaskhokhar999 • 80 • updated 5 days ago by Asaf ♦ 7.2k
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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 6 days ago by waqaskhokhar999 • 80
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Extract longest ORF
... I have input file contains multiple nucleotide sequences in fasta format. I am using a standalone Linux version of [ORFfinder][1] using following command: /Path/ORFfinder -in /Path_to_input_file/input_file.fasta -s 0 -out output_fasta -outfmt 0 This generates output file containing all ORF, b ...
rna-seq written 6 days ago by waqaskhokhar999 • 80 • updated 6 days ago by Fatima • 510
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Comment: C: Alternative of ORFFinder for multiple nucleotide sequences
... Many thanks, Can you please suggest me how I can design loop for it? ...
written 28 days ago by waqaskhokhar999 • 80
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Alternative of ORFFinder for multiple nucleotide sequences
... I have a file that contains multiple sequences in Fasta format. I am interested to translate them and want only protein sequences for the longest ORF. I can do this using [ORFFinder][1] but I have to process each sequence individually as it doesn't support multiple sequences. Is there any alternati ...
orf translation rna-seq written 29 days ago by waqaskhokhar999 • 80 • updated 29 days ago by genomax ♦ 79k
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Comment: C: Find gene ids based on genome coordinates
... Many thanks for your response, I have checked the reason for ids that don't match. I have estimated the AS events from assemblies generated by stringtie. The coordinates in stringtie vary from TAIR10 coordinates, so I need to extract the gene coordinates from stringtie assembly and then have to assi ...
written 5 months ago by waqaskhokhar999 • 80

Latest awards to waqaskhokhar999

Supporter 28 days ago, voted at least 25 times.
Popular Question 16 months ago, created a question with more than 1,000 views. For Alternative splicing events in transcriptomic data
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