User: mt1022

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mt1022180
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China
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3 years, 4 months ago
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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 10 weeks ago by mt1022180
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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 9 months ago by mt1022180
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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 12 months ago by mt1022180
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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 17 months ago by mt1022180
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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 19 months ago by mt1022180 • updated 19 months ago by wuchangcheng6620
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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 21 months ago by mt1022180
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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 22 months ago by mt1022180
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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 23 months ago by mt1022180 • updated 22 months ago by Tom_L310
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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 23 months ago by mt1022180
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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 23 months ago by mt1022180

Latest awards to mt1022

Appreciated 12 months ago, created a post with more than 5 votes. For A: Difference between GTF file with CHR and without CHR. ENSEMBL
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Difference between GTF file with CHR and without CHR. ENSEMBL
Supporter 15 months ago, voted at least 25 times.
Popular Question 18 months ago, created a question with more than 1,000 views. For what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean
Popular Question 18 months ago, created a question with more than 1,000 views. For get case submitter ID for GDC miRNA quantification files
Student 21 months ago, asked a question with at least 3 up-votes. For get case submitter ID for GDC miRNA quantification files
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: get case submitter ID for GDC miRNA quantification files
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: get case submitter ID for GDC miRNA quantification files

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