User: epigene

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epigene390
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United States
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3 days, 10 hours ago
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4 years, 8 months ago
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Posts by epigene

<prev • 85 results • page 1 of 9 • next >
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Answer: A: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
... I realized that I asked this question 3 years ago. Now I've got a bit more experience and would like to share some of my personal thoughts on the question. 1. Learn by doing. I ended up picking up most of what I know by working on the problems and trying to find answers from the internet, mostly f ...
written 8 months ago by epigene390
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Comment: C: Subsample BAM to fixed number of alignments
... sample tool looks really cool. but i have a question on `samtools reheader nohead_reads_1M_sample.sam reads.bam` step, nohead_reads_1M_sample.sam doesn't have header and `samtool reheader` is supposed to use input sam header to modify input bam file. So this line doesn't make sense, right? ...
written 10 months ago by epigene390
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Comment: C: how do aligners determine which reads to apply duplicate reads flag (1024)?
... I understand.. I should have been more careful with the right terms as there are important distinctions. ...
written 13 months ago by epigene390
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Comment: C: how do aligners determine which reads to apply duplicate reads flag (1024)?
... I didn't say they have the same read name..and they don't. I meant for the seq and quality. Yeah, after BWA, the bam file was feed to Picard's MarkDuplicates tool. Thanks for the explanations. ...
written 13 months ago by epigene390
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how do aligners determine which reads to apply duplicate reads flag (1024)?
... I was trying to understand how aligners, specifically bwa, determine which reads to apply the 1024 flag in the sam output. I notice I have cases where two identical reads (same read seq and same quality scores) are mapped to different locations on yeast chr16 as shown below: Mxxx:1:2103:26709 ...
sam bwa written 13 months ago by epigene390 • updated 13 months ago by dariober8.2k
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Comment: C: PE read flag 69 and 137 meaning
... thanks for the answer, I was apparently confused with the meaning of flag 4 and 8. ...
written 14 months ago by epigene390
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PE read flag 69 and 137 meaning
... I'm very confused with the meaning of flag 69 and 137. From the explain flag tool https://broadinstitute.github.io/picard/explain-flags.html flag 69 (1+4+64) means: read paired read unmapped first in pair flag 137 (1+8+128) means: read paired mate unmapped ...
flag sam written 14 months ago by epigene390 • updated 14 months ago by harold.smith.tarheel3.9k
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Comment: C: How To Filter Mapped Reads With Samtools
... i agree with 5heikki's comment for filtering mapped PE reads if mapped means either both read and mate mapped or either mapped. From what I tested with pysam, this is their default definition of mapped in the fetch() function. Edit: I changed my mind and realized that the command -f4 -F 8 doesn't ...
written 14 months ago by epigene390
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Comment: C: Where to download earlier versions of GWAS Catalog?
... yeah, thanks for the comment! ...
written 15 months ago by epigene390
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Tools to analyze Illumina's HumanHT-12 v4 microarray expression data?
... I got some gene expression data based on Illumina's HumanHT-12 v4 Expression microarray kit. The goal is to find differentially expressed genes. Does anyone have recommendations on tools to use to analyze the data? Could be a standalone package or R package or anything decent. Thanks! ...
gene expression microarray written 15 months ago by epigene390

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Great Question 5 months ago, created a question with more than 5,000 views. For what does a high derived allele frequency mean?
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Popular Question 14 months ago, created a question with more than 1,000 views. For RNA-Seq: does stranded and directional mean the same thing?
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