User: leo1985.arnab

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Posts by leo1985.arnab

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Comment: C: Print line based on partial match
... Sparrow_kop the script is working. Thanks ! But only if the sequences are in the same order in both files. I did mistakenly write previously that the total number of sequences in 2 files are identical, actually they are not. Apologies. File 2 with the larger sequences has many many more sequences. B ...
written 6 weeks ago by leo1985.arnab0
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Comment: C: Print line based on partial match
... Shenwei, thanks for the reply. But I already tried that grep option before posting the topic. It didn't work. ...
written 6 weeks ago by leo1985.arnab0
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Print line based on partial match
... I have two files with several hundred entries in each. File 1 has several 5 base seqeunces and file 2 has higher number of entries but with longer sequences. The first 5 bases of sequences in file 2 matches that of file 1. I tried some grep and awk methods , but did not work out for a partial match ...
sequence written 6 weeks ago by leo1985.arnab0
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Comment: C: Sequence extraction based on coordinates
... Thanks a lot for the solution Alex !! ...
written 5 months ago by leo1985.arnab0
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Sequence extraction based on coordinates
... I have a file with sequences in first column and start coordinate for these sequences in the 3rd column. I want to extract all rows where the starting loci of sequences vary by 5 nt of each other. Following is an example Sequence Column header_xxx Start coordinate ...
sequence written 5 months ago by leo1985.arnab0 • updated 5 months ago by Alex Reynolds21k
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Comment: C: Count of mapped reads
... Okay thanks. Yes, that is what I want. Sorry if that was not clear from my writing. I will try BBMap then. ...
written 5 months ago by leo1985.arnab0
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Comment: C: Count of mapped reads
... Oops- apologies for posting incorrectly. Thanks for the suggestion. The sequences in the fasta file are between 22-30 nucleotides in length. I am going to try out featureCounts and see how that goes. Thanks ! ...
written 5 months ago by leo1985.arnab0
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Comment: A: Count of mapped reads
... Yes @genomax. you are correct. I want to know for every sequence how many different places it can map to and then report the total number of mapped hits for that sequence. This eventually translates into total number of mapped reads for that sequence. ...
written 5 months ago by leo1985.arnab0
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Count of mapped reads
... Hello, I have around 12,000 smallRNA reads (sequences) for which I need to find the total mapped reads for EACH individual sequence. They are in a collapsed fasta file ensuring the sequences appear only once in the entire file (trimming and quiality filtering etc have been already done ). I want to ...
sequence written 5 months ago by leo1985.arnab0
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Comment: C: Nucleotide character position in sequence extract
... Wonderful ! Thanks ! That worked out great. Just needed to remove the -m1 at the end as I wanted to search through the whole file. ...
written 5 months ago by leo1985.arnab0

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