User: bioinfo8

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bioinfo880
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Posts by bioinfo8

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Comment: C: Rename headers of multiple fasta files inside loop
... Thanks, it will take only one fasta file at a time. My aim is to extract the genes with similar gene name from all the fasta files and make gene specific fasta files with updated header including gene name and file name (so that I should know from which file that gene came) + append the gene sequenc ...
written 13 hours ago by bioinfo880
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Comment: C: Rename headers of multiple fasta files inside loop
... Thanks. But, I want to combine with `pyfasta` so that I can extract gene from each sample file + add sample name (file name) to header in one step. Can you suggest some easier way, such as `awk, sed` etc. As `awk` is working for one file and I did not do any linerization eventhough that file is mult ...
written 3 days ago by bioinfo880
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Comment: C: Rename headers of multiple fasta files inside loop
... Header from sample1.fasta file >gene_name1 ATGC..............................max upto 120 characters per line TTTG.............................................................. >gene_name2 ATGG.............................................................. . ...
written 3 days ago by bioinfo880
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Rename headers of multiple fasta files inside loop
... Hi, I have 10 fasta files (each file with 20 gene sequences from each of the 10 samples). I would like to create 20 files, specific to each gene from 10 samples. I proceeded as follows to extract genes with the file_name in header: pyfasta extract --header --fasta test.fasta gene_name1 | awk ...
fasta pyfasta header gene bash written 3 days ago by bioinfo880
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Comment: C: Extract Sequence From Fasta File Using Ids From A Separate File
... @matted Would you please elaborate? ...
written 3 days ago by bioinfo880
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Comment: C: Extract Sequence From Fasta File Using Ids From A Separate File
... @Bulbul Did you find the solution? ...
written 3 days ago by bioinfo880
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Answer: A: which one is good mafft or clustalW???
... My first preference is always [ClustalX][1] (for more sequences) and [Clustal Omega][2] (for few sequences). For extensive analysis, [MEGA][3] is awesome. But, one should always try to use 2 or more tools to validate the output. [1]: http://www.clustal.org/clustal2/ [2]: http://www.ebi.ac.uk ...
written 5 days ago by bioinfo880
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Comment: C: Converting bam -> fasta
... @diviya.smith Did you find the solution? ...
written 5 days ago by bioinfo880
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Comment: C: convert bam to clustal
... Thanks, but its not that helpful. ...
written 5 days ago by bioinfo880
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Comment: C: convert bam to clustal
... Yes, I did and it showed alignments and file is quite big (as there are multiple reads >1000). I realized that I need consensus sequence from all the reads for that region and then can align consensus sequence with reference gene. How to get consensus sequence from all reads? ...
written 5 days ago by bioinfo880

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Centurion 5 days ago, created 100 posts.
Supporter 3 months ago, voted at least 25 times.

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