User: ATpoint

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ATpoint5.5k
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#! /usr/bin/Rscript

class(ATpoint)

> [1] 50% wet-lab rat

> [2] 50% wannaba computational biologist


cat(Research_Interests)

> Impact of somatic mutations on the non-coding genome

Posts by ATpoint

<prev • 733 results • page 1 of 74 • next >
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Comment: C: bwa-mem, from .sam/.bam to fasta file
... Of course. BAM is a binary (compressed) version of the SAM format. The default output of BWA is SAM. bwa mem (options...) > out.sam samtools sort out.sam -o out_sorted.bam Or more elegant: bwa mem (...) | samtools sort -o out_sorted.bam ...
written 1 hour ago by ATpoint5.5k
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Comment: C: bwa-mem, from .sam/.bam to fasta file
... Really, STAR does that? Ok good to know, that means I will never use aligned BAM files from STAR to get back the original reads in fastq format. Thanks for letting me know :-D ...
written 1 hour ago by ATpoint5.5k
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Answer: A: bam-readcount not finding reference in bam file
... > @SQ SN:reference_1:1-35911 LN:35911 > Blockquote As you can see from this line, the chromosome name is reference_1:1-35911, not reference_1. Change that in your reference_1_regions.txt. Are you trying to get an output for an entire BAM file? What do you want to do with it. The only use of t ...
written 5 hours ago by ATpoint5.5k
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Comment: C: If a string appears twice in column 1, select the higher value in column 2
... You're very welcome! ...
written 5 hours ago by ATpoint5.5k
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Answer: A: deeptools bamcompare/bamcoverage merging bins?
... Why don't you split the genome into bins of 100bp (bedtools `makewindows`), and then use `featureCounts` (or similar tools) to get the counts per bin directly from the bam files? Once you have this, you can use awk to normalize the bins to RPKM and get the mean with `bedtools` map ## Calculate ...
written 16 hours ago by ATpoint5.5k
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Answer: A: If a string appears twice in column 1, select the higher value in column 2
... Removing the % from $4, then sorting $4 in descending numeric order and choosing only unique IDs of $1 gives the intended output. The advantage of this over any if/else iterative script that checks the lines after the current one for other occurrences of the same $1 is that the input is not required ...
written 16 hours ago by ATpoint5.5k
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Comment: C: bwa-mem, from .sam/.bam to fasta file
... > The size of the bam depends on how many reads mapped to the reference That is not true. All reads will be at the SAM/BAM file, they simply will be flagged as unmapped. Still, default (and only) output of BWA mem is SAM not BAM. Simply count reads in one of the fastq files (`wc -l fastq.fastq`) ...
written 23 hours ago by ATpoint5.5k
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Comment: C: Reheadering a subsetted bam gives truncated file
... Ok, never heard of this strategy. Thanks! ...
written 1 day ago by ATpoint5.5k
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Comment: C: Reheadering a subsetted bam gives truncated file
... > I mapped against a merged genome of human and mouse Do you have a reference that this is good practice and reliable? I could imagine that because of homologies between the species, you'll get plenty of multimappers. ...
written 1 day ago by ATpoint5.5k
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Comment: C: question about identifying differential expressed genes in TCGA
... @OP, the point with using arbitrary thresholding like you do is that every NGS experiment has something called a mean-variance relationship. That means that genes (or regions or whatever you measure) may have high variation/enrichments because of small counts (here lowly expressed genes). These guys ...
written 1 day ago by ATpoint5.5k

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Teacher 3 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 3 days ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Teacher 6 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 8 days ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Scholar 14 days ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Commentator 14 days ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Scholar 20 days ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Teacher 20 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
Teacher 23 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
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Teacher 4 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
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Help in regard of sequencing data
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Scholar 5 weeks ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Commentator 5 weeks 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 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
Scholar 7 weeks ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Teacher 7 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
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Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
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