User: mt1022

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mt1022170
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China
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Posts by mt1022

<prev • 20 results • page 1 of 2 • next >
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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 6 months ago by mt1022170
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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 9 months ago by mt1022170
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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 14 months ago by mt1022170
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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 16 months ago by mt1022170 • updated 16 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 18 months ago by mt1022170
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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 19 months ago by mt1022170
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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 20 months ago by mt1022170 • updated 20 months ago by Tom_L270
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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 20 months ago by mt1022170
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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 20 months ago by mt1022170
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how to adjust size of intervals in bed12 format?
... I have a file containing genomic intervals in bed12 format. I want to adjust the size of each interval (specifically, remove N base from both end of each interval). `bedtools slop` seems only works with bed6. Is there a convenient way to achive this for bed12 intervals? ...
bedtools bed alignment written 20 months ago by mt1022170 • updated 20 months ago by Carlo Yague4.2k

Latest awards to mt1022

Appreciated 9 months ago, created a post with more than 5 votes. For A: Difference between GTF file with CHR and without CHR. ENSEMBL
Good Answer 9 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 13 months ago, voted at least 25 times.
Popular Question 15 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 15 months ago, created a question with more than 1,000 views. For get case submitter ID for GDC miRNA quantification files
Student 18 months ago, asked a question with at least 3 up-votes. For get case submitter ID for GDC miRNA quantification files
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: get case submitter ID for GDC miRNA quantification files
Teacher 23 months 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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