User: bk11

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bk1140
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Posts by bk11

<prev • 55 results • page 1 of 6 • next >
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Comment: C: Merging bed bim fam files from chromosome 1 to 22 at one time
... @khn How did you solve this problem? I am also new to plink. I am facing the same problem. How can we merge multiple binary files of different chromosomes using plink? ...
written 11 months ago by bk1140
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Comment: C: Problem with newSCESet(countData=all.counts) function
... Thank you Santosh. `library(scater)` was loaded and still could not find function `"newSECSet"` ...
written 12 months ago by bk1140
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Problem with newSCESet(countData=all.counts) function
... Hi, I m running through [this][1] for single cell RNAseq data analysis. And I got this error after running a few codes. If some one could figure out that what might have I done wrong, I will appreciate. Thanks library(R.utils) gunzip("GSE61533_HTSEQ_count_results.xls.gz", remove=FALSE, over ...
single cell experiment single cell rna seq written 12 months ago by bk1140 • updated 12 months ago by Santosh Anand5.0k
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Answer: A: Select number for each region
... cat file1.txt chr1:10041971-10153500 chr2:2644661-293334 chr2:32120816-32177000 chr20:27254237-27374800 chr10:706059-1034630 chr3:215840607-215890726 chr5:4353812-4477220 cat file2.txt 1 chr1:10041971-10153500 2 chr1:10745944-10994508 3 chr2:2644661-29 ...
written 12 months ago by bk1140
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Comment: C: target gene selection for miRNA
... If you have list of differentially expressed mRNA from the same sets of samples, it will be easier to narrow down your target genes based on their opposite expression patterns. ...
written 13 months ago by bk1140
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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 13 months ago by bk1140
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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 13 months ago by bk1140
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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 13 months ago by bk1140 • updated 13 months ago by Alex Reynolds29k
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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 13 months ago by bk1140
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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 13 months ago by bk1140

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