User: husensofteng

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husensofteng90
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Sweden
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1 week, 3 days ago
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1 year ago
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Posts by husensofteng

<prev • 15 results • page 1 of 2 • next >
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Answer: A: Keeping only common variants in the merged VCF file
... I am not sure if I understand the question correctly, but it sounds as a line filtering issue to me. So: awk '$1~"#" || ($3~"rs" && $3~"chr")' inputfile > outputfile *Only keep lines that start with # (header lines) or there is rs ID and chr info at the third column of the file. ...
written 4 weeks ago by husensofteng90
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Answer: A: get GTEx mean expression by tissue
... You could use this file instead, it has the tissue names in the header: [Gene expression (TPM ) median per tissue type][1], note it is median not mean! [1]: https://storage.googleapis.com/gtex_analysis_v7/rna_seq_data/GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_median_tpm.gct.gz ...
written 4 weeks ago by husensofteng90
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Comment: C: Checking regions with high density of SNPs
... this answer might be useful: https://www.biostars.org/p/379113/#379121 ...
written 6 weeks ago by husensofteng90
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Comment: C: Stringtie merge assembly with extra transcripts
... yes sure, but remember the expression values are for the whole transcript. Also, stringTie uses a maximum flow algorithm to use all sequencing reads therefore the alternative transcripts are not necessarily real ones and hence further validation is needed. May be you also want to consider exon-cent ...
written 6 weeks ago by husensofteng90
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Answer: A: Mapping SNP position to gff file
... one way is to use the [intersect][1] function from [BedTools][2]. awk 'BEGIN{FS=OFS="\t"}{if(NR>1){ print $1,$2-1,$2 }}' snps.txt | bedtools intersect -wb -a genes.gtf -b stdin | awk '$3=="gene"' 1. first converts your SNP list into a BED file (chr, start, stop) and removes the header ...
written 6 weeks ago by husensofteng90 • updated 6 weeks ago by ATpoint18k
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Answer: A: Stringtie merge assembly with extra transcripts
... The two extra ones are potentially novel transcripts according to StringTie. However, StringTie tries to assemble all reads in each loci: when a known transcript can explain the reads it just reports the known transcript. Whereas in cases of remaining reads, it tries to assemble other transcript for ...
written 7 weeks ago by husensofteng90
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Job: Front-end developer for research and cancer personalized medicine platforms
... We need a new team member to join the Cancer proteomics Mass spectrometry (MS) research group led by Janne Lehtiö at Karolinska Institutet in Stockholm, Sweden We seek an all-round front-end developer to contribute in developing tumor board decision support systems, web-based visualization software ...
javascript web-portal job front-end html written 8 weeks ago by husensofteng90
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Comment: C: compare two columns of two files
... another tip is to use sort and join commands. ...
written 9 weeks ago by husensofteng90
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Comment: C: Annotation of noncoding variants and transcription factor motifs
... Thank you so much ATpoint for these valuable points. I have gone through them all and I have tried to fix the errors. I just learned that it's possible to do spell corrections directly in vim (:set spell spelllang=en_us) :) We hope to manage rerunning the pipeline on hg38 and incorporating the more ...
written 3 months ago by husensofteng90
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Answer: A: How to access specifically 30x NA12878 sequencing runs
... [SRA explorer][1] returns several projects on SRA that have the WGS raw data for NA12878. You could type NA12878 in the search box and add the desired results to the collection, then you get direct links to the fastq files from the save datasets button at the top of the page. However, to identify w ...
written 3 months ago by husensofteng90

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