User: Grinch

gravatar for Grinch
Grinch60
Reputation:
60
Status:
New User
Location:
Germany
Last seen:
2 weeks, 2 days ago
Joined:
4 years ago
Email:
s**********@gmail.com

Posts by Grinch

<prev • 26 results • page 1 of 3 • next >
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Comment: C: ATAC-seq fragment length distribution
... Surprisingly not. More than 95% were paired, out of those more than 50% were properly paired. I would also expect much lower numbers. To me, it looks as if someone has half way sorted the files by forward/reverse reads, but not completely. I find it hard to believe that these are the files directly ...
written 9 weeks ago by Grinch60
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Answer: A: ATAC-seq fragment length distribution
... For anyone looking at this post in the future, I will explain how I solved this issue: The issue was in the raw data I was given. The data, as i mentioned above was PE sequencing and i was given two files per sample, marked as _1 and _2, and the information that these are forward and reverse reads. ...
written 9 weeks ago by Grinch60
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Comment: C: Correct GC bias using read counts and Loess regression method
... for MacOS users, use gsed instead if sed, otherwise you will get an error `sed: 1: "1i chr\tstart\tend\tGC\tRC": command i expects \ followed by tex` ...
written 9 weeks ago by Grinch60
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Answer: A: Bed file with the snoRNA coordinates
... This is an older post, but for people searching through BioStar in the future, use RNAcentral for the most comprehensive database on snoRNAs or any other ncRNA type. You can download FASTA or BED or GTF files, for your species and/or RNA type. For example all human snoRNAs, https://rnacentral.org/se ...
written 4 months ago by Grinch60
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Comment: C: Extract a chromosome from a WIG file
... It produces an empty file. I checked with grep and the chromosome exists in the original file. ...
written 10 months ago by Grinch60
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Comment: C: Extract a chromosome from a WIG file
... Thank you. I knew there had to be a simple solution like this available. ...
written 10 months ago by Grinch60
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Extract a chromosome from a WIG file
... I have a large WIG files which are difficult to run in IGV, due to the size. I am only interested in chromosome M so I would like to extract signal from that chromosome and thus have a smaller file size. I found one solution on Stackoverflow (https://stackoverflow.com/questions/17354962/pcregrep-a-w ...
wig written 10 months ago by Grinch60 • updated 9 months ago by EagleEye6.4k
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Comment: C: ATAC-seq fragment length distribution
... I've added the information in the description. ...
written 11 months ago by Grinch60
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Comment: C: ATAC-seq fragment length distribution
... I've added the information in the description. ...
written 11 months ago by Grinch60
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ATAC-seq fragment length distribution
... Hi, I'm analyzing **human cancer cell line** ATAC-seq data (PE 75bp Illumina) and have encountered a weird insert size distribution. For ATAC-seq PE data, insert size distribution is a good quality control of how well the experiment worked (This is how it would ideally look https://dbrg77.wordpress ...
atac-seq written 11 months ago by Grinch60

Latest awards to Grinch

Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: ATAC-seq fragment length distribution
Scholar 9 weeks ago, created an answer that has been accepted. For A: ATAC-seq fragment length distribution
Popular Question 4 months ago, created a question with more than 1,000 views. For MeDIP-seq and hMeDIP-seq analysis
Great Question 6 months ago, created a question with more than 5,000 views. For Generating the output file name from the input file in bash script
Popular Question 22 months ago, created a question with more than 1,000 views. For MeDIP-seq and hMeDIP-seq analysis
Popular Question 23 months ago, created a question with more than 1,000 views. For MeDIP-seq and hMeDIP-seq analysis
Supporter 23 months ago, voted at least 25 times.
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Generating the output file name from the input file in bash script

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