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2 votes

Convert paired-end BAM into a single-end BAM and keep all the reads

MRNM stands for "Mate reference index". So Picard found something in the RNEXT field which should be set only for paired-end reads but the rest of the file looks like single-end. The ...
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2 votes

Convert paired-end BAM into a single-end BAM and keep all the reads

Like Devon pointed out, most likely you should sort out whether the files have been marked for duplicates correctly. You can also use samtools rmdup too ...
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2 votes

Biological replicates on Chip-seq Transcription factor data

This question is somewhat generic, so a generic answer is that ENCODE has a Transcription Factor ChIP-seq Data Standards and Processing page that can give you a useful starting point. For TF ChIP-seq ...
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2 votes

Biological replicates on Chip-seq Transcription factor data

You could first look at the degree of correlation between the two replicates - what proportion of peaks are shared between the two, versus peaks found in one sample only? This will give an idea of ...
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2 votes

Score predefined ChIP-seq peaks with MACS2 or equivalent

You could try setting a high p-value threshold when you're calling peaks to retain the "non-significant" values. Something like: ...
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2 votes
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How to visualize called narrowPeak files in UCSC Genome browser or IGV?

I think you might have changed the separator (or at least have some kind of inconsistency from the required format) for your file. Note that peak output files from MACS2 are variants of BED files. It ...
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2 votes
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How to get the intersection of peaks after peak calling using MACS2?

bedtools intersect with multiple files after -b performs pairwise intersections between -a ...
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2 votes

merging two/or more bed file into one bed file

In my opinion, the easiest way to merge bed files is to use bedtools merge.
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1 vote

merging two/or more bed file into one bed file

Convert each of your Excel spreadsheets to tab-delimited text files (how-to). Install and run Cygwin, if using Windows. If you are using OS X, open up the Terminal app. Install the BEDOPS toolkit to ...
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1 vote

Separating peaks of chip-seq with specific length

You can use rtracklayer from R bioconductor to import it, filter and do much more stuff, i use the code from this blog for ...
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1 vote
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Separating peaks of chip-seq with specific length

You can do it by awk. awk -v OFS="\t" '{ if ( ($3-$2) >= 500 && ($3-$2) <= 1000) { print } }' in.bed > out.bed Assuming there is no ...
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1 vote

differential analysis of chip-seq data

For sharing, you can test the proportion of overlapping peaks using bedtools intersect or the find.overlap function in ...
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1 vote

How to make Venn diagram for the Macs peak calling output of two data sets?

Venn diagrams can be helpful, but for peak calling they can be somewhat misleading. This topic is addressed in the DiffBind documentation, in the "Comparison of occupancy and affinity based analyses" ...
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1 vote

How to make Venn diagram for the Macs peak calling output of two data sets?

Check out the tool Intervene. It's exactly designed for this. Github link.
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1 vote
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gnu parallel for macs peak calling

not gnuparallel but nextflow. I don't know macs and what is 'first.bam' and 'second.bam' is not clear not me but I hope you'll get the idea. The nextflow: ...
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1 vote

When running ChIPQC bioconductor package after peak calling, should I use sorted BAM files or unsorted BAM files?

You need to provide sorted bam files, ideally with an index. If you run ChIPQCsample, it calls ChIPQC:::sampleQC which iterates ...
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1 vote

ATAC-seq macs2 peak splitting in sliding windows

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