User: shenwei356

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shenwei3563.4k
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China
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http://shenwei.me/
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Posts by shenwei356

<prev • 419 results • page 2 of 42 • next >
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Comment: C: Replace _ in sequences with variant allele in fasta header
... If it helps, please upvote and accept this answer. ...
written 3 months ago by shenwei3563.4k
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Comment: C: fastq.gz goes into gz cpgz loop
... What's the output of `file xxx.tar` and `file xxxx.gz`. You can also ask for help from the service provider. ...
written 3 months ago by shenwei3563.4k
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Answer: A: Replace _ in sequences with variant allele in fasta header
... That's not that hard by matching the SNPs and flanking sequences using a regular expression. To make it easy to process, let's linearize the FASTA sequences, i.e. converting to tabular format. For example: $ seqkit fx2tab seqs.fa 2|28804|28804|rs544393009|dbSNP|C/T TGCAT_TCAGC Hereb ...
written 3 months ago by shenwei3563.4k
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Comment: C: Extracting Fasta sequences
... that's interesting. check this https://en.m.wikipedia.org/wiki/FASTA_format it's not a FASTA format. you need write some scripts to handle this special format. yes you do. ...
written 3 months ago by shenwei3563.4k
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Comment: C: Extracting Fasta sequences
... just paste the main error message here ...
written 3 months ago by shenwei3563.4k
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Comment: C: If it's possible for R detecting the reverse compliment sequence?
... then retrive sequences not starting with ATG, compute the revcom sequences and cat them to those starting with ATG. a shell solution: seqkit grep -s -i -p ^ATG seqs.fa > positive.fa seqkit grep -s -i -p ^ATG -v seqs.fa | seqkit seq -r -p > processed.fa cat positive.fa proc ...
written 3 months ago by shenwei3563.4k
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Comment: C: Extracting Fasta sequences
... what's the error? Try provide more information when giving feedback. I guess you did not install the tool, haha ...
written 3 months ago by shenwei3563.4k
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Comment: C: Extracting Fasta sequences
... There are lots of similar posts in this site, please search before asking. seqkit grep --by-name --use-regexp --pattern tRNA-Phe seqs.fa ...
written 3 months ago by shenwei3563.4k
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Comment: C: Extracting Fasta sequences
... have you try anything? ...
written 3 months ago by shenwei3563.4k
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Comment: C: How to add the suffix if the entries are the same in fasta file
... http://bioinf.shenwei.me/seqkit/usage/#rename seqkit rename seqs.fa > new.fa ...
written 3 months ago by shenwei3563.4k

Latest awards to shenwei356

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 3 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 3 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 6 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 6 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 7 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 7 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 7 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 7 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 7 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 8 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 8 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Scholar 8 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 8 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 8 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 9 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus

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