User: blur
blur • 150
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Posts by blur
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... Hi,
I am doing ribo_seq analysis and I aligned my files (R1+R2) to the rRNA, then I took the resulting reads that were not aligned to the rRNA (turned the sam to one fastq file) and aligned them with tophat2 to the genome. This is my cmd:
tophat2 -G BioMart.GRCh37.75.gtf -o ./output 3 -p 3 -- ...
written 18 days ago by
blur • 150
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Comment:
C: No coverage in macs2 peak summit!
... I did
The bam matches the IGV, the macs results do not ...
written 6 weeks ago by
blur • 150
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Comment:
C: No coverage in macs2 peak summit!
... The files used in IGV and to create the BAM files are the same file.
The genome used is mm10 (mouse)
the coverage in other areas is normal, there are peaks that look OK
I loaded BAM files ...
written 6 weeks ago by
blur • 150
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Comment:
C: No coverage in macs2 peak summit!
... yes, same release, same source, same file ...
written 6 weeks ago by
blur • 150
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171
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Comment:
A: No coverage in macs2 peak summit!
... https://ibb.co/2qG9grQ ...
written 6 weeks ago by
blur • 150
0
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171
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Comment:
C: No coverage in macs2 peak summit!
... https://ibb.co/2qG9grQ ...
written 6 weeks ago by
blur • 150
0
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0
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171
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Comment:
C: No coverage in macs2 peak summit!
... There is not much to show
The IGV plot is empty - no reads... ...
written 6 weeks ago by
blur • 150
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... I have a weird problem
I ran macs2 to read peaks and got a list of peaks and peak summits
The cmd was:
macs2 callpeak -t IP.bam -c input.bam -f BAM -g 994080837 --bw 100 --keep-dup all --nomodel -n WT -B -q 0.01
I was looking at IGV to see the peaks and I see areas indicated as summits were t ...
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... Hi,
I have 2 experiments, each with 10 peak files in bedtools format.
My idea was to check which peaks are repeated in 6/10 experiments in group 1 - I'll call the results group1_repeated.bed, Then 6/10 in group 2 to created group2_repeated.bed
The idea is then to compare group1_repeated.bed to gro ...
written 9 weeks ago by
blur • 150
• updated
9 weeks ago by
Alex Reynolds ♦ 31k
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... I will answer my own question :)
I ran this with --dovetail as per the bowtie2 manual and to make sure it makes sense I used the protocol's original "--local --very-sensitive- local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700"
The results were almost identical (alignment rates were a ...
written 11 weeks ago by
blur • 150
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