User: Chunjie Liu

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Chunjie Liu90
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90
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Location:
US, Houston
Website:
http://chunjie-sam-liu...
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an hour ago
Joined:
2 months, 2 weeks ago
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Posts by Chunjie Liu

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Extract surrounding genome sequences given certain locations using R
... Thanks for your correctness. This is a simple example for using biomaRt. The previous version of Ensembl support 'chr' character. You can choose the Ensembl release or genome build by `useMart` or `useEnsembl`. The Ensembl give the [tutorial][1]. [1]: http://useast.ensembl.org/info/data/biomar ...
written 11 hours ago by Chunjie Liu90
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Answer: A: Extract surrounding genome sequences given certain locations using R
... You can use [biomaRt][1] GENES = useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "useast.ensembl.org") YouRange<- getBM(attributes = c("chromosome_name", "start_position", "end_position"), filters = c("chromosome_name","start","end"), values = list(chromosome_n ...
written 18 hours ago by Chunjie Liu90
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Answer: A: How To Map Ucsc Mrna Isoforms To Gene ?
... Use `biomaRt` library(biomaRt) GENES = useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl") getBM(attributes = c('ensembl_gene_id','hgnc_symbol','ensembl_transcript_id','refseq_mrna','ucsc','chromosome_name','transcript_start','transcript_end'), mart = GENES) ...
written 4 days ago by Chunjie Liu90
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Comment: C: Concatenate Sequence Fragments in Multiple Alignment Fasta
... Use bash loop, grep and sed one line command can deal with this problem. I give the sed part. ...
written 7 days ago by Chunjie Liu90
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Answer: A: Concatenate Sequence Fragments in Multiple Alignment Fasta
... You may try `sed -n '/NM_152486.2_hg19/{n;p}' refGene.fa |tr -d '\n'` ...
written 7 days ago by Chunjie Liu90
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Answer: A: Obtain Ensembl transcript ids that contain retained introns
... If you are familiar with R, I recommend you '[biomaRt][1]', you can use intron position to find nearest transcript and get Ensembl transcript ID. Hope it help! [1]: https://bioconductor.org/packages/release/bioc/html/biomaRt.html ...
written 8 days ago by Chunjie Liu90
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Answer: A: Error while downloading data using SRA toolkit
... You may check this [post][1], I use lftp to download SRA data. [1]: https://www.biostars.org/p/227184/#227234 ...
written 13 days ago by Chunjie Liu90
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Answer: A: PlantTFDB and PlantRegMap: Plant Transcription Factor Database and Plant Regulat
... Provide a comprehensive animal transcription factor database [AnimalTFDB][1]. A vedio user guide for [AnimalTFDB v1][2] [1]: http://bioinfo.life.hust.edu.cn/AnimalTFDB/index.php [2]: http://blog.openhelix.eu/?p=13225 ...
written 26 days ago by Chunjie Liu90
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Answer: A: Your Favorite Bioinformatics Blogs (March 2010)
... It can't be regarded as blog, but it's hub of bioinformatics software and databases [https://omictools.com/][1]. [1]: https://omictools.com/ ...
written 26 days ago by Chunjie Liu90
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Answer: A: Batch download of hg19 sequences in bed file
... From your script, you want to download all hg19 fasta, then use bedtools to extract from fasta. Your script is not correct. for chr in `seq 1 22` X Y M do wget -O - -q http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr${chr}.fa.gz & done wait gunzip -c * ...
written 4 weeks ago by Chunjie Liu90

Latest awards to Chunjie Liu

Scholar 8 days ago, created an answer that has been accepted. For A: Obtain Ensembl transcript ids that contain retained introns

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