User: nim.1111.ou

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nim.1111.ou160
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Posts by nim.1111.ou

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Comment: C: Bash One-liners collection on Github
... bioinformaticians think alike ;) I have been collecting the commands for years i think its time to share. Since I was also the system admin of my lab, my notes include one-lines for data processing and Linux administration. ...
written 17 months ago by nim.1111.ou160
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Tutorial: Bash One-liners collection on Github
... I started working on bioinformatics a few years ago (recently switched to cloud computing), and was amazed by those single-word bash commands which are much faster than my dull scripts, time saved through learning command-line shortcuts and scripting. Not all the code here is oneliner, but i put eff ...
bash-oneliners tutorial bash shell linux bioinformatics written 17 months ago by nim.1111.ou160 • updated 12 months ago by cionsystemsi0
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Comment: C: Generate more splice variant from RNA-seq data
... we are from bioinformatics lab, and the RNA-seq data are collected from different experiments from different databases, i think most are not stranded. We apply a [pipeline][1] which will generate new transcripts, achieving our initial attempt to increase the number of isoforms, yet we worry if biolo ...
written 3.8 years ago by nim.1111.ou160
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Comment: C: Generate more splice variant from RNA-seq data
... thank you very much for your detail answer! what do you think about a whole new exon appear before or after the annotated gene region? Actually they make up large portion of our output. I've checked that some of them overlap with nearby gene while some are completely unannotated. if i removed them ...
written 3.8 years ago by nim.1111.ou160
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Answer: A: Update third line in fastq file using Biopython
... what do you mean by update? i love using bash for editing files sed 's/^+/+something/g' //edit the lines start with a '+' into start with '+something' ...
written 3.8 years ago by nim.1111.ou160
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Generate more splice variant from RNA-seq data
... Our lab are working on alternative splicing event in some non-model organisms however, there are few mRNA (transcripts) in the annotation files, 1 transcript per gene in most cases. We thought that it is because the genome is poor annotated, so we collect a lot RNA-seq data and apply Hisat and Stri ...
stringtie isoforms rna-seq alternative splicing written 3.8 years ago by nim.1111.ou160
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Answer: A: Useful Bash Commands To Handle Fasta Files
... ive been working on bioinformatics for over three years, here are lots of frequently used bash commands [https://github.com/onceupon/Bash-Oneliner/blob/master/README.md][1] [1]: https://github.com/onceupon/Bash-Oneliner/blob/master/README.md ...
written 4.2 years ago by nim.1111.ou160
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Comment: C: paper reference of SRA dataset
... oic, thank you so much! ...
written 5.2 years ago by nim.1111.ou160
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paper reference of SRA dataset
... Hello,  i am new in bioinformatics, i was wondering when i download a SRA dataset, for example, with accession number :SRX265467, how can i locate the published paper of that data? Thank you   ...
sra references dataset written 5.3 years ago by nim.1111.ou160 • updated 5.3 years ago by Kamil2.0k

Latest awards to nim.1111.ou

Popular Question 17 months ago, created a question with more than 1,000 views. For paper reference of SRA dataset
Appreciated 17 months ago, created a post with more than 5 votes. For Bash One-liners collection on Github
Popular Question 3.4 years ago, created a question with more than 1,000 views. For paper reference of SRA dataset

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