User: blur

gravatar for blur
blur150
Reputation:
150
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Trusted
Location:
European Union
Last seen:
1 day, 9 hours ago
Joined:
6 years ago
Email:
b***@pazcorp.com

Posts by blur

<prev • 162 results • page 1 of 17 • next >
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TopHat2 --prefilter-multihits option gives supp. alignments?
... 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 -- ...
tophat2 --prefilter-multihits written 18 days ago by blur150
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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 blur150
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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 blur150
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Comment: C: No coverage in macs2 peak summit!
... yes, same release, same source, same file ...
written 6 weeks ago by blur150
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Comment: A: No coverage in macs2 peak summit!
... https://ibb.co/2qG9grQ ...
written 6 weeks ago by blur150
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Comment: C: No coverage in macs2 peak summit!
... https://ibb.co/2qG9grQ ...
written 6 weeks ago by blur150
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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 blur150
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No coverage in macs2 peak summit!
... 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 ...
macs2 peaks written 6 weeks ago by blur150 • updated 4 days ago by Biostar ♦♦ 20
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compare two groups of multiple bed files
... 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 ...
bedtools bedfiles written 9 weeks ago by blur150 • updated 9 weeks ago by Alex Reynolds31k
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Comment: C: Cut & run - bowtie2 dovetail option
... 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 blur150

Latest awards to blur

Great Question 15 days ago, created a question with more than 5,000 views. For Generate consensus from BAM file
Popular Question 4 months ago, created a question with more than 1,000 views. For UCSC peak calling - weird results
Popular Question 4 months ago, created a question with more than 1,000 views. For UCSC peak calling - weird results
Popular Question 4 months ago, created a question with more than 1,000 views. For where can I find more data about --outSAMattributes All?
Popular Question 7 months ago, created a question with more than 1,000 views. For UCSC peak calling - weird results
Popular Question 7 months ago, created a question with more than 1,000 views. For Bcftools magic string
Popular Question 7 months ago, created a question with more than 1,000 views. For UCSC peak calling - weird results
Popular Question 7 months ago, created a question with more than 1,000 views. For Bcftools magic string
Popular Question 8 months ago, created a question with more than 1,000 views. For cutadapt --cut option for paired-end reads?
Great Question 10 months ago, created a question with more than 5,000 views. For Generate consensus from BAM file
Popular Question 10 months ago, created a question with more than 1,000 views. For cutadapt --cut option for paired-end reads?
Popular Question 10 months ago, created a question with more than 1,000 views. For Bcftools magic string
Popular Question 11 months ago, created a question with more than 1,000 views. For Generate consensus from BAM file
Popular Question 11 months ago, created a question with more than 1,000 views. For bcftools soft filters (-s)
Popular Question 18 months ago, created a question with more than 1,000 views. For Generate consensus from BAM file
Popular Question 18 months ago, created a question with more than 1,000 views. For MACS2 and duplicates
Popular Question 18 months ago, created a question with more than 1,000 views. For bcftools soft filters (-s)
Popular Question 18 months ago, created a question with more than 1,000 views. For fastq_quality_trimmer: Premature End-Of-File
Popular Question 23 months ago, created a question with more than 1,000 views. For Generate consensus from BAM file
Popular Question 23 months ago, created a question with more than 1,000 views. For uneven paired end reads in bowtie
Popular Question 23 months ago, created a question with more than 1,000 views. For BWA vs. bowtie
Popular Question 23 months ago, created a question with more than 1,000 views. For cutadapt --cut option for paired-end reads?
Popular Question 23 months ago, created a question with more than 1,000 views. For MACS2 and duplicates
Popular Question 23 months ago, created a question with more than 1,000 views. For FASTX error - quality score
Popular Question 2.2 years ago, created a question with more than 1,000 views. For The bed12 format

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