User: murathong

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murathong100
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China
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2 years, 3 months ago
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Posts by murathong

<prev • 18 results • page 1 of 2 • next >
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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 3 months ago by murathong100
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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 5 months ago by murathong100 • updated 5 months 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 7 months ago by murathong100
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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 8 months ago by murathong100
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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 9 months ago by murathong100 • updated 9 months ago by Tom_L210
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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 9 months ago by murathong100
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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 9 months ago by murathong100
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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 9 months ago by murathong100 • updated 9 months ago by Carlo Yague3.2k
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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 10 months ago by murathong100
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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 14 months ago by murathong100

Latest awards to murathong

Supporter 8 weeks ago, voted at least 25 times.
Popular Question 4 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 4 months ago, created a question with more than 1,000 views. For get case submitter ID for GDC miRNA quantification files
Student 7 months ago, asked a question with at least 3 up-votes. For get case submitter ID for GDC miRNA quantification files
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: get case submitter ID for GDC miRNA quantification files
Teacher 12 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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