User: Sparrow_kop

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Sparrow_kop90
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90
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China
Last seen:
18 hours ago
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2 years, 1 month ago
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m******@163.com

Posts by Sparrow_kop

<prev • 16 results • page 1 of 2 • next >
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Comment: C: NCBI genome annotation compatible with HISAT
... You just want to align the reads to transcriptom, so you need not to change coordinates. Also, the chromosome name can be 'chr1' or '1', you can just simple use the genome fasta to get the index file by hisat. Then hisat do everything for you. ...
written 9 days ago by Sparrow_kop90
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Answer: A: Scripting solution to generate a list of KEGG ORTHOLOGY (KO) terms from a tab-de
... In python, I assume the delimiter is tab with open('your_file','r') as f: for line in f: if 'KO:' in line: line = line.strip().split('\t') print(line[0] + '\t' + line[1].split(':')[-1]) ...
written 9 days ago by Sparrow_kop90
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Comment: C: Aligning RNA seq data to genome or transcriptome
... If the genome is model genome, in RNA-seq, the mainstream is to map to the transcriptome, which can great help to guide the splice site identification. ...
written 10 days ago by Sparrow_kop90
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Comment: C: FASTA file into excel file format?
... You want to convert fasta file to excel file? So you need to do analysis in windows? If you use python , it is very easy to convert to excel format file using the "Openpyxl" package. Such as the column 1 is the id, the column 2 is the short sequence. But if the file is huge, I think it is not a goo ...
written 10 days ago by Sparrow_kop90
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Comment: C: Automated method to translate DrugBank Biological Entity (BE) drug target IDs to
... Well, in my own experience, from drugbank database, drug DB_id and its target Gene symbol are enough for me, I never used BE id ... Meanwhile, despite the BE info is not mentioned in your url, it existing in the xml file indeed, and followed by the uniprot id. For example , in the full_database.xml ...
written 15 days ago by Sparrow_kop90
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Comment: C: differentially expressed miRNA
... Hi, you can try DESeq2 or edgeR which based on count values. They are the mainstreaming tools currently to do DE analysis. ...
written 15 days ago by Sparrow_kop90
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Answer: A: Automated method to translate DrugBank Biological Entity (BE) drug target IDs to
... Hi, in fact, if you can access to the full_database.xml from drugbank, all info you need is contained in it, for example "BE identifier" ,"UniProt". So you can parse the xml and match the target tags to get the info you want if you want to do web scraping. ...
written 15 days ago by Sparrow_kop90
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Comment: C: Print line based on partial match
... Hi, I think I don't get it , what's the meaning of 'same order', you mean you want match the reverse complementation? Or you means the sequence order, for example the alphabetical order? If it is the latter one, the order does not matter, because for each loop, grep will match the pattern on the ...
written 15 days ago by Sparrow_kop90
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Answer: A: Print line based on partial match
... Hi, because "The first 5 bases of sequences in file 2 matches that of file 1. " So 'grep -f file1 file2' is not so robust, because the pattern may be exist in other location other than the first 5 base. So you can use regular expression in bash : #!/bin/bash cat file1.txt | while read pat ...
written 15 days ago by Sparrow_kop90
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Answer: A: Gene annotation help
... Hi, they are different version of genome assembly, the former is hg19 or Grch37, the latter one is hg18, so different version has different coordinate. I suggest you use hg19 or hg38, which is better than hg18, you can download from UCSC Genome or [Ensembl][1]. [1]: http://www.ensembl.org/index. ...
written 15 days ago by Sparrow_kop90 • updated 15 days ago by Emily_Ensembl13k

Latest awards to Sparrow_kop

Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Gene annotation help
Scholar 15 days ago, created an answer that has been accepted. For A: Gene annotation help

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