User: mt1022

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mt1022210
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Posts by mt1022

<prev • 21 results • page 1 of 3 • next >
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Answer: A: strand specificity of TFBS
... Have a look at this article: [Lis M, Walther D. The orientation of transcription factor binding site motifs in gene promoter regions: does it matter? BMC Genomics. 2016 Mar 3;17:185. doi: 10.1186/s12864-016-2549-x. PubMed PMID: 26939991][1]. > Our results suggest that for the motifs considered ...
written 20 months ago by mt1022210
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Comment: C: Difference between GTF file with CHR and without CHR. ENSEMBL
... In my opinion, use either one is OK for normal DE analysis. However, if you do not want to loose information about any annotated gene, use the one without 'chr'. (And sorry for the late response). ...
written 2.3 years ago by mt1022210
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Answer: A: Software for Mcdonald-Kreitman test
... Standard MK test is influenced by population demography and selective forces acting on nearby sites. Asymptotic estimate of alpha has been shown closer to real alpha based on simulations (Messer & Petrov 2013). There is also a web server to calculate asymptotic alpha (http://benhaller.com/messer ...
written 2.5 years ago by mt1022210
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Answer: A: Where to find Download version of GRCh37 in NCBI
... ENSEMBL has a dedicated site for GRCh37 with annotations files updated about every 6 months: http://grch37.ensembl.org/index.html ...
written 2.9 years ago by mt1022210
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how to display RNA-seq coverage data in negative strand with log scale?
... Coverage data for negative strand is displayed as negative values in igv. Is there a way to display those data in log scale? For example, if the coverage is -3, I would like it to be displayed as -log(3). ...
rna-seq igv written 3.1 years ago by mt1022210 • updated 3.1 years ago by wuchangcheng6630
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Answer: A: Difference between GTF file with CHR and without CHR. ENSEMBL
... The one without 'chr' contains annotations for genes on unplaced or unlocalized contigs, while the one with 'chr' only contains annotation for assembled chromosomes, both of them have no prefix 'chr' in chromosome name, see this example: zcat Danio_rerio.GRCz10.87.gtf.gz | cut -f1 | awk '{dict[ ...
written 3.2 years ago by mt1022210
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Comment: C: why allelic count on forward and reverse strand do not add up to depth in the re
... the quality of base calling for those reads is ~30 at that position. I guess this is not the main problem. ...
written 3.3 years ago by mt1022210
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why allelic count on forward and reverse strand do not add up to depth in the results of samtools mpileup?
... dmel_mitochondrion_genome 2878 . A <*> 0 . DP=15;I16=0,9,0,0,347,13419,0,0,180,3600,0,0,140,2570,0,0;QS=1,0;MQ0F=0 PL:ADF:ADR 0,27,86:0,0:9,0 See the above line for example. Here the depth is DP=15, however allelic count on forward strand and reve ...
vcf samtools mpileup written 3.4 years ago by mt1022210 • updated 3.3 years ago by Tom_L320
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Comment: C: how to adjust size of intervals in bed12 format?
... I didn't intend to slop each block. For example, if first block is 8nt in length, I want to discard this block and then remove 2 nt from next block so that I removed 8 + 2 nt = 10nt in total. Anyway, I have written a script for this: [bed12_slop.py][1]. I haven't test it on all possible extreme cond ...
written 3.4 years ago by mt1022210
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Comment: C: how to adjust size of intervals in bed12 format?
... Hi. You should consider the size of each block (column 11). if the first block is shorter than 10, then the start should adjusted based on the original start and the start position of the next block (start posn of each block is in column 12). ...
written 3.4 years ago by mt1022210

Latest awards to mt1022

Popular Question 19 months ago, created a question with more than 1,000 views. For where can I get the parameters used by UCSC genomes to run RepeatMasker for dm6?
Popular Question 19 months ago, created a question with more than 1,000 views. For what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean
Scholar 19 months ago, created an answer that has been accepted. For A: Difference between GTF file with CHR and without CHR. ENSEMBL
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: Difference between GTF file with CHR and without CHR. ENSEMBL
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Popular Question 3.0 years ago, created a question with more than 1,000 views. For what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean
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