User: ATpoint

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ATpoint3.9k
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Last seen:
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Joined:
2 years, 1 month ago
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#! /usr/bin/Rscript

class(ATpoint)

> [1] 50% wet-lab rat

> [2] 50% wannaba computional biologist


cat(Research_Interests)

> Mutational impact on non-coding parts of cancer genomes.

Posts by ATpoint

<prev • 529 results • page 1 of 53 • next >
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Comment: C: how to find new transcript from bam file?
... Do you try to get smallRNAs from standard RNA-seq or from smallRNA-seq? ...
written 2 days ago by ATpoint3.9k
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Comment: C: kmer content failling with fastqc
... You did not link a picture, and might read [this][1] first. [1]: https://www.biostars.org/p/172860/ ...
written 2 days ago by ATpoint3.9k
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Comment: C: ChIP-seq analysis ( QC)
... I use skewer to trim fastq files for a trailing base quality of 30, and an average base quality of the read of 25. Use fastqc to get an idea of the low-level data quality. ...
written 2 days ago by ATpoint3.9k
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Comment: C: Varscan somatic caller - Genotype calls
... Ok, latest version is 2.4.3. I posted my suggested workflow using VarScan recently today [here][1], you should be able to adapt it one-to-one. I suggest you re-run it on your sample with the latest version of the program (maybe on a subset of your BAM including the region you posted). Note that you ...
written 3 days ago by ATpoint3.9k
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Comment: C: Varscan somatic caller - Genotype calls
... The header line you posted has 10 fields, but line 2 has 12. Please post the full command line, and the version of VarScan (I assume you used VarScan2, latest version right)? Did you do any postprocessing of the primary call set? ...
written 3 days ago by ATpoint3.9k
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Comment: C: fastx_clipper problem in output
... Yes, skewer does all in one go. A typical command line for single-end data Illumina data could be: ./skewer -n -q 25 -Q 25 in.fastq.gz It removes reads with excessive Ns (-n), removes bases at the 3' end until it hits a base with quality > 25 (-q 25) and discards reads with an average base ...
written 3 days ago by ATpoint3.9k
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Answer: A: germline calling of tumor-normal paired sample germline by varscan2
... I recommend the following command line. It makes a combined tumor-normal mpileup and pipes it into VarScan2, applying the strand-filter, and leaving everything else at default. Be sure to use the latest varscan version. ## 1. Get the raw variants: samtools mpileup -q 20 -Q 25 -B -d 1000 -f ...
written 3 days ago by ATpoint3.9k
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Comment: C: visualizing the file with BigWig format
... IGV definitely supports BW format. Please check if you have the current version of IGV, and point out how these BWs have been generated, and what the error message is. ...
written 3 days ago by ATpoint3.9k
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Answer: A: assemble 3 SRA files for a single species
... My suggestion: ## 1. Use fastq-dump on each of the files, e.g. parallelized with GNU parallel: ls *.sra | parallel "fastq-dump --gzip --split-3 {}" ## 2. Check files with fastqc: ls *.fastq.gz | parallel "fastqc {}" ## 3. If metrics are ok, combine them: cat SRR*_1 ...
written 3 days ago by ATpoint3.9k
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Comment: C: fastx_clipper problem in output
... Do not use fastx-toolkit in 2018. It is not actively being maintained and does not support paired-end data (as far as I know). Currently accepted options are bbdup.sh from BBMap, trimmomatic, cutadapt or skewer (the latter is my go-to choice). ...
written 3 days ago by ATpoint3.9k

Latest awards to ATpoint

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Scholar 2 days ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Commentator 8 days ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Commentator 18 days ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Commentator 24 days ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Scholar 6 weeks ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Scholar 3 months ago, created an answer that has been accepted. For A: what is the purpose of indexing a genome
Scholar 3 months ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Scholar 3 months ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Scholar 3 months ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner

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