User: cpad0112

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Posts by cpad0112

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Comment: C: MEGAN Group Comparison
... For future reference: http://megan.informatik.uni-tuebingen.de/t/how-to-compare-groups/415 ...
written 2 hours ago by cpad01128.9k
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Comment: C: how to find out which cellular pathways a gene belongs to?
... For pathways, KEGG and for functions in a cell, try GO:MF ...
written 7 hours ago by cpad01128.9k
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Comment: C: Genomic coordinates from traditional HGVS variants
... Try ensembl variation api ...
written 14 hours ago by cpad01128.9k
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Comment: C: GRCh37.p13 download at NCBI FTP?
... Download GRCh37.p13 single fasta file from Gencode: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/GRCh37.p13.genome.fa.gz or from here with index as well: http://bioinfo.hpc.cam.ac.uk/downloads/datasets/fasta/grch37/ ...
written 1 day ago by cpad01128.9k
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Comment: C: Parsing header of FASTA File
... Assuming that fasta is linearized (i.e sequence is in single line, after header): sed -n '/>/p' test.fa | grep -vw chromosome | grep --no-group-separator -f - -A 1 test.fa should give you all the fasta sequences with no chromosome in header. sed -n '/>/p' test.fa | grep -w chromoso ...
written 1 day ago by cpad01128.9k
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Answer: C: EMBOSS transeq translate to protein with 3 letter code
... > The output peptide sequence is always in the standard one-letter > IUPAC code. http://structure.usc.edu/emboss/transeq.html and try this: $ echo atgtttcaggacccacaggagtaa | showseq -filter -threeletter y -format 4 10 20 ----:----|----:----|---- ...
written 1 day ago by cpad01128.9k
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Answer: C: Error in pheatmap: formal argument "scale" matched by multiple actual arguments
... `scale = "row"` and `scale = "none"` in conflict in your function, you defined them twice. ...
written 1 day ago by cpad01128.9k • updated 1 day ago by zx87545.0k
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Answer: C: Remove text and keep '> + ID' in fasta file
... a little late to the party: $ sed '/>/ s/^.*__\(\w\+\)__.*/>\1/g' file.fa or $ sed '/>/ s/^\(\W\).*__\(\w\+\)__.*/\1\2/g' file.fa >778568 GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAACTGAGAGTCGGCGATGAGCAGCCGGA GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAA >778569 GCT ...
written 2 days ago by cpad01128.9k
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Comment: C: how to change fasta headers?
... try this: https://www.biostars.org/u/21479/ $ sed '/>/ s/^\(>\w\+.\w\).*/\1/g' file.fa or $ sed '/>/ s/^\(.*\.\w\).*/\1/g' file.fa >WP_000580188.1 MIGQQRNILATLGIDVWIPRTQVCQKNNAHTLWRDQVVEPHESITVPTIDVPAFEQKNTQPQVLEIPKVVEEPPIVVAEVSQPEILVEKPKVIEQETITPFELQAYCLEKCVIFVDVTAL ...
written 2 days ago by cpad01128.9k
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Answer: A: how to change fasta headers?
... $ sed '/>/ s/.*_\([A-Z]\{2\}_[0-9]\+.[0-9]\).*/>\1/g' test.fa or $ sed '/>/ s/.*=\([A-Z]\+_[0-9]\+.[0-9]\).*/>\1/g' test.fa >WP_000637306.1 MIVSNNFAVPYYLNVRKEKGMTAYYWATHQSQLALFDSYELAYRFYFPSRHILIRSEIKAFAQ >WP_000572517.1 MIEQIQKRSLVDEVIHVIRQNIKNDIWKVDEKI ...
written 2 days ago by cpad01128.9k

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Scholar 1 day ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 1 day ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
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Commentator 22 days ago, created a comment with at least 3 up-votes. For C: Problem installing Rgraphviz in R
Scholar 23 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 5 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 6 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 6 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
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Appreciated 7 weeks ago, created a post with more than 5 votes. For C: can someone read this result to me
Scholar 7 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 7 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 7 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 9 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change

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