User: Explorer

gravatar for Explorer
Explorer10
Reputation:
10
Status:
New User
Location:
Canada
Last seen:
5 days, 3 hours ago
Joined:
8 months, 3 weeks ago
Email:
e***********@gmail.com

Posts by Explorer

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Subseq a FASTA file
... I am not sure about that. When I open it in a text editor, there are blocks of 60nt each while in SnapGene, ApE it is as per software settings. I got confused because the code suggested for multiline sort-of worked. In the original thread shared by Pierre Lindenbaum, the following code was suggeste ...
written 10 days ago by Explorer10
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Comment: C: Subseq a FASTA file
... It seems SeqKit is more memory efficient. I will try it if bash does not work. ...
written 11 days ago by Explorer10
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Comment: C: Subseq a FASTA file
... Thanks for sharing the link. I tried the command for multiline FASTA and it partially worked. I am extending the thread there. ...
written 11 days ago by Explorer10
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Comment: C: Extraction of nt bases from sequence
... I am trying this code for a big file. Just as an example first 4 sequences, each 30000 nucleotide When I try the following code, it works. awk '/^>/{print;getline;print substr ($0, 20, 25)}' NCBIaligned.fasta > out.fasta >NC_045512.2 Severe acute respiratory syndrome coronav ...
written 11 days ago by Explorer10
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Subseq a FASTA file
... I am trying to subsetting a FASTA file at a specific nucleotide positions. For example >random sequence 1 tatgtgcgag >random sequence 2 agggtgttat >random sequence 3 tatgtgcgag >random sequence 4 gactcgcggt >random ...
sed awk written 12 days ago by Explorer10
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Comment: C: Unique sequences in FASTA file (with count and IDs)
... I am trying to learn R but if there is a simpler command in awk, I would really appreciate it if you may share. ...
written 12 days ago by Explorer10
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Comment: C: Unique sequences in FASTA file (with count and IDs)
... Thank you. Changing data from DNAstring to dataframe works perfectly. I am wondering is there a way to determine frequency along with count in the code? ...
written 19 days ago by Explorer10
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Unique sequences in FASTA file (with count and IDs)
... I am trying to find unique sequences along with count and IDs from a FASTA file in R using Biostring. For exmaple >random sequence 1 tatgtgcgag >random sequence 2 agggtgttat >random sequence 3 tatgtgcgag >random sequence 4 gactcgcggt >random sequen ...
R sequence alignment written 20 days ago by Explorer10 • updated 20 days ago by zx87549.9k

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