User: murathong

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murathong60
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China
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Posts by murathong

<prev • 15 results • page 1 of 2 • next >
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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 10 days ago by murathong60
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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 7 weeks ago by murathong60 • updated 4 weeks ago by Tom_L80
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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 7 weeks ago by murathong60
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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 7 weeks ago by murathong60
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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 7 weeks ago by murathong60 • updated 7 weeks ago by Carlo Yague2.2k
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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 12 weeks ago by murathong60
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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 6 months ago by murathong60
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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 7 months ago by murathong60
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Comment: C: where can I get the parameters used by UCSC genomes to run RepeatMasker for dm6?
... hi, following the archives by genome@soe.ucsc.edu, I find the answer after looking up similar posts. [how ucsc do RepeatMasker][1] my $defaultSpecies = 'scientificName from dbDb'; my $species = $opt_species ? $opt_species : &HgAutomate::getSpecies($dbHost, $db); Thanks for your help! ...
written 11 months ago by murathong60
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Comment: C: where can I get the parameters used by UCSC genomes to run RepeatMasker for dm6?
... Thanks. I am interested in whether UCSC genome browser will additionly use the '-species' parameter to specify the species/clade or only use '-s' for all species as it is not mentioned in the FAQ. I am not sure whether '-species' parameter will improve the results. ...
written 11 months ago by murathong60

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Teacher 4 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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