User: david.fear

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david.fear10
Reputation:
10
Status:
New User
Location:
European Union
Last seen:
3 years, 6 months ago
Joined:
4 years, 1 month ago
Email:
d*********@kcl.ac.uk

Posts by david.fear

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Merge Bam files
... Sorry, how do you merge with different read groups, there doesn't seem to be an option for that using merge bam files in SAM tools?   ...
written 4.1 years ago by david.fear10
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Answer: A: Merge Bam files
... Thanks. I'll give it a go.   ...
written 4.1 years ago by david.fear10
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Answer: A: Merge Bam files
... I don't think so ...
written 4.1 years ago by david.fear10
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Comment: C: Merge Bam files
... Yes, they had been.   ...
written 4.1 years ago by david.fear10
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Tool: Merge Bam files
... I am trying to merge 3 .bam files (different alignments of the same ChIP-seq run), one has 5.9M reads, one 1.2M and one 0.4M. However after running merge bam files in sam tools I only get back a file with 4.2M reads in it (at least the output of rmdup tells me I have 4.2M reads). Any ideas as to why ...
samtools tool written 4.1 years ago by david.fear10
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SICER Failed to
... I have been trying to run SICER on my ChIP-seq data set. Seequnces were aligned with bowtie2, sequencing errors and duplicates removed. The resultant .bam files were converted to .Sam and format changed to .bed. However when I try to run SICER I get an error. What am i doing wrong? I have pasted a ...
chip-seq written 4.1 years ago by david.fear10 • updated 4.1 years ago by Jennifer Hillman Jackson25k
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Answer: A: rmdup - remove PCR duplicates from ChIP-seq data
... Hi, Thanks for your reply, how is this different from rmdup in SAM tools? Dave   ...
written 4.1 years ago by david.fear10
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rmdup - remove PCR duplicates from ChIP-seq data
... I have aligned my chip-seq data with bow tie and wanted to remove PCR duplicates. I ran rmdup in SAM tools on the aligned file but the number or reads I got back (i.e.. 8787256 / 9006759 = 0.9756 in library) was more than the number of single aligned reads I started with? I assume these numbers are ...
chip-seq samtools written 4.1 years ago by david.fear10 • updated 4.1 years ago by Jennifer Hillman Jackson25k

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