User: bk11

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bk1130
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Posts by bk11

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Comment: C: bedtools complement error
... Could you please show your command lines who you generated bed files? I am still having problem. ...
written 15 days ago by bk1130
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Comment: C: bedtools complement error
... I changed it into tab-delimited and still does not work. sed 's/ /\t/g' my.genome >my.genome1 cat my.genome1 chr1 1000 chr2 800 ...
written 15 days ago by bk1130
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bedtools complement error
... Hi I have an error from bedtools. What might be happening? I have two bed files: cat A.bed chr1 100 200 chr1 400 500 chr1 500 800 cat my.genome chr1 1000 chr2 800 when I run this: bedtools complement -i A.bed -g your.genome It gives Error: The gen ...
bedtools written 15 days ago by bk1130 • updated 14 days ago by Alex Reynolds26k
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Comment: C: How to identify RNA-seq mapped reads to reference genome but not identified by f
... Hi, Earlier I defined exon and gene_id features of reference gtf file in the featureCount. It looks like other regions that can be defined are: **CDS, five_prime_utr, gene, Selenocysteine, start_codon, stop_codon, three_prime_utr and transcript.** How can I define intronic and intergenic reads? ...
written 15 days ago by bk1130
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Comment: C: How to identify RNA-seq mapped reads to reference genome but not identified by f
... When I changed the strand selector from -s2 to -s0 in featureCount, the assigned read count were doubled i.e. from 10-12% to 20-25%. It is still very low exonic reads. ...
written 15 days ago by bk1130
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How to identify RNA-seq mapped reads to reference genome but not identified by featurecounts of Subread package?
... Hi We have performed RNA-seq of 60 sorted T cells from human and aligned to the reference genome (GRCh38) using HISAT2. About 80% of reads were mapped to the reference genome. However, when featureCounts of Subread package was used to count mapped reads, only 20-25% of mapped reads were counted to ...
featurecounts rna-seq hisat2 written 15 days ago by bk1130 • updated 15 days ago by kristoffer.vittingseerup1.0k
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Comment: C: awk and sed in bash script and no output
... It worked very nicely though. ...
written 4 weeks ago by bk1130
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Comment: C: awk and sed in bash script and no output
... I tried sending the result to .txt file but also it did not work. ...
written 4 weeks ago by bk1130
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Comment: C: awk and sed in bash script and no output
... Yes the text files have 16 columns: Group Sub-group Name Sex Cell type Tissue Cell line Disease Donor Experiment File type Format Analyis production Size MD5 URL bone marrow band form neutrophil BM030613 Male band form neutrophil bone marrow None BM030613 H3K27ac Normalized signal bigWig E ...
written 4 weeks ago by bk1130
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Comment: C: awk and sed in bash script and no output
... Yes I am running the script in the same directory that has the text files. This is related to bioinformatics as it is used to get URL to download histone proteins binding signals from different cell types. ...
written 4 weeks ago by bk1130

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