User: murathong

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murathong90
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China
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1 year, 11 months ago
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Posts by murathong

<prev • 17 results • page 1 of 2 • next >
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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 7 weeks ago by murathong90 • updated 7 weeks ago by wuchangcheng6610
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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 months ago by murathong90
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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 4 months ago by murathong90
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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 5 months ago by murathong90 • updated 5 months ago by Tom_L180
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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 5 months ago by murathong90
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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 5 months ago by murathong90
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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 5 months ago by murathong90 • updated 5 months ago by Carlo Yague2.9k
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Answer: A: Implementing McDonald-Kreitman test
... I met the same problem recently and I assign assign equal weight to all possible mutation path. For example, for TTC to CTA, TTC->TTA->CTA and TTC->CTC->CTA have the same probability, as I am dealing triplet change in noncoding region. The following article talks more sophiscated method ...
written 6 months ago by murathong90
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Answer: A: get case submitter ID for GDC miRNA quantification files
... following the instruction on https://gdc-docs.nci.nih.gov/API/Users_Guide/Search_and_Retrieval I figured out how to download the uuid and barcode associated with each miRNA quantification file. first determine how many files there are ```curl 'https://gdc-api.nci.nih.gov/files/ids?query=mirnas.qua ...
written 10 months ago by murathong90
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get case submitter ID for GDC miRNA quantification files
... I downloaded hundreds of miRNA quantifications files from GDC and wanted to analyze its association with clinical information. The problem is how to get corresponding sumitter ID (previous TCGA barcode) of each file. This is an example: https://gdc-portal.nci.nih.gov/files/b2804bb2-70f4-471a-b6db- ...
uuid tcga gdc mirna written 11 months ago by murathong90

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Popular Question 16 days ago, created a question with more than 1,000 views. For what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean
Popular Question 20 days ago, created a question with more than 1,000 views. For get case submitter ID for GDC miRNA quantification files
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Teacher 8 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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