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bedtools multiple BAM files

bedtools shellscript bamtobed written 18 days ago by amitpande74 • 0

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622

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Bamtobed paired mate error

bedtools bed bedops bamtobed written 14 months ago by rbronste • 360 • updated 14 months ago by ATpoint ♦ 42k

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622

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Is BED file generated by bametobed sorted ?

bedtools ngs bamtobed coverage sequencing written 2.2 years ago by pacman • 50 • updated 2.2 years ago by Alex Reynolds ♦ 31k

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3.8k

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How to interpret the outputs generated from bamtobed using BedTools?

bedtools bed bam bamtobed written 5.4 years ago by Louis Kok • 20 • updated 5.4 years ago by Sukhdeep Singh ♦ 10k

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Recent Replies

C: research options avalaible using rna-seq datasets for an undergraduate by ATpoint ♦ 42k
You should get a supervisor to give you a project that is managable in the time you have availabl...
A: Obtaining SNPs with large samples in a short time by Pierre Lindenbaum ♦ 131k
Create a GVCF file for each samples in a 'small genomic region" with gatk haplotypecaller in GVCF...
C: Obtaining SNPs with large samples in a short time by Kevin Blighe ♦ 68k
These are whole-genome BAMs? Please add more information
A: What happens if a UMI fragment has a PCR artefact? by ATpoint ♦ 42k
That is a common problem in sequencing and specialized software addressing sequencing errors im U...
A: Novel protein identification by Qiongyi • 10
A general guide is: If you find a predicted protein which is not previously documented (e.g. not ...
C: Manipulating a fasta file to only have specificcharacters by Qiongyi • 10
GO TO https://github.com/Qiongyi/custom_PERL_scripts/ AND THEN FIND linker.pl
C: Demultiplexing 10x fastq files by GROUPS of barcodes by bds1217 • 0
`umi-tools` actually worked great and was way easier than I was expecting it to be. I thought I w...
C: What happens if a UMI fragment has a PCR artefact? by _r_am ♦ 31k
Do not add an answer unless you're answering the top level post. Use `Add Comment` or `Add Reply`...
A: What happens if a UMI fragment has a PCR artefact? by asumani • 70
I see. That wrong UMI created during a PCR amplification.And that single read with wrong UMI will...
C: Is there a way to use multiple processors (parallelize) to create a heatmap for by _r_am ♦ 31k
Unfortunately, no. If the package is not designed to use multiple cores, there's not much you can...
C: Creating gtf file? by opplatek • 40
What do you need a gtf for and what kind of information do you think it should contain? Since you...
A: How to convert realign BAM file into fastq file by opplatek • 40
Based on the other comments `samtools fixmate` didn't help so it seems you have some singleton re...

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