User: jgbradley1

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jgbradley1100
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100
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New User
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United States
Last seen:
3 years, 11 months ago
Joined:
5 years, 1 month ago
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Posts by jgbradley1

<prev • 21 results • page 1 of 3 • next >
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Answer: A: Samtools mpileup not providing correct count info
... I figured out the solution myself. I had simulated more error in my reads than I initially thought  For anyone else experiencing a similar issue, check the -Q, --min-BQ mpileup flag. Samtools automatically does not count reads in the other tags unless they are "high quality" (i.e. have a minimum bas ...
written 4.3 years ago by jgbradley1100
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Samtools mpileup not providing correct count info
... I simulated reads for a list of variant sites using GATK SimulateReadsForVariants tool. From that, I get a bam file output. Next I create a pileup using samtools mpileup. samtools mpileup -t DP,DPR,DV,INFO/DPR -vuf GRCh37.fa -l snp.file.vcf simreads.bam > simreads.raw.vcf The problem is that t ...
simulation samtools mpileup pileup written 4.3 years ago by jgbradley1100
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Comment: C: How to align a sequence with a pair of sequence DNA?
... Here's a naive approach that may help you understand what others have already mentioned. I think there are more issues that you need to be aware of when looking at this problem. Suppose you have 1 set of paired-end reads (2 different sequences), then you can align each sequence separately to your re ...
written 4.3 years ago by jgbradley1100
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Comment: C: Using rna-seq, why map reads to the genome but calculate gene expression by alig
... For my specific use case, I am using ensembl annotations from biomart for human. If you know R, it's not too difficult to read in the annotations and then filter for the aligned reads that span an exon region. ...
written 4.4 years ago by jgbradley1100
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Comment: C: Using rna-seq, why map reads to the genome but calculate gene expression by alig
... I just found this discussion about the same issue of gene quantification using the genome .vs transcriptome. I agree with Alex Dobin's opinion when he said "...there are dangers in mapping the reads only to the annotated transcript sequences, since a large number of reads (~25%) usually map outside ...
written 4.4 years ago by jgbradley1100
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Using rna-seq, why map reads to the genome but calculate gene expression by aligning to the transcriptome?
... Skip to the last paragraph to go straight to the question. I am interested in looking at variants from a rna-seq sample of GM12878 and comparing to variants found by GIAB. The basic outline of my pipeline is the following 1) Trim reads with ngShoRT. 2) Align reads with STAR to the reference genome ...
genome rna-seq transcriptome written 4.4 years ago by jgbradley1100 • updated 15 months ago by Tom K20
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Answer: A: Parallelized mpileup script
... I just want to point readers to new tool, Sambamba that I found, It's essentially a wrapper around Samtools and Bcftools that parallelizes jobs when possible. It's currently in development but I have been happy with the results so far. It's worth checking out. It also parallelizes 'bcftools view' op ...
written 4.4 years ago by jgbradley1100
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Comment: C: Difference Between Samtools And Gatk Algorithms
... Although an old post, I wanted to add a few helpful links for anyone visiting this post again and wanting a more mathematical explanation of the samtools/bcftools algorithms. Multiallelic calling algorithm in bcftools Mathematical notes on samtools algorithms I found these links in the publicatio ...
written 4.4 years ago by jgbradley1100
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What are acceptable SNP QUAL and GQ thresholds to filter on?
... I have been trying to figure out what are acceptable thresholds to filter SNPs on. I'm using GATK HaplotypeCaller and the distribution of QUAL scores that I see look like   The huge peak of SNPs at QUAL ~1000 looks odd to me, but I have seen this same distribution in both a human and dog sample, ...
qual threshold snp written 4.5 years ago by jgbradley1100 • updated 4.5 years ago by Len Trigg1.3k
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Answer: A: How do I configure the read name output from STAR?
... For anyone that comes here, I was never able to find a parameter in STAR (v2.4.0k) that would easily allow for this. STAR reads in the sequence id from a fastq file up until the first space character (not the entire line). My solution was to reformat the sequence id's in the fastq file before mappin ...
written 4.6 years ago by jgbradley1100 • updated 13 months ago by RamRS24k

Latest awards to jgbradley1

Scholar 4.3 years ago, created an answer that has been accepted. For A: How do I configure the read name output from STAR?
Scholar 4.6 years ago, created an answer that has been accepted. For A: How do I configure the read name output from STAR?

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