User: Grinch

gravatar for Grinch
Grinch70
Reputation:
70
Status:
Trusted
Location:
Germany
Last seen:
13 hours ago
Joined:
4 years, 5 months ago
Email:
s**********@gmail.com

Posts by Grinch

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Distribution of mapped reads
... I don't understand why you want to annotate lncRNAs in smallRNA-seq data? You won't find any or rather you shouldn't if the library preparation was done properly. You also wrote in the comment that you enriched for miRNAs and piRNAs. Neither of these have introns. ...
written 3 months ago by Grinch70
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Answer: A: Distribution of mapped reads
... Firstly, for small RNAs you should use Bowtie2 or similar, for mapping reads, because small RNAs don't have introns, thus a spliced aligner is not necessary, in fact it performs worse in my experience for such data. After the alignment of reads to the reference genome, you should count number of rea ...
written 3 months ago by Grinch70
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Comment: C: Calling differential peaks on large set of 3 conditions
... FYI DiffBind uses both DESeq and EdgeR, based on user's choice. ...
written 3 months ago by Grinch70
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Answer: A: Calling differential peaks on large set of 3 conditions
... I would recommend DiffBind R package which in my hands works best for MEDIPS or ChIP-seq analysis with replicates and/or multiple conditions. MACS2 bdgdiff also works well, but then I would do an additional step afterward to see which are the common peaks between replicates, which you can do with ID ...
written 4 months ago by Grinch70
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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 7 months ago by Grinch70
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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 7 months ago by Grinch70
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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 7 months ago by Grinch70
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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 9 months ago by Grinch70
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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 15 months ago by Grinch70
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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 15 months ago by Grinch70

Latest awards to Grinch

Teacher 7 months ago, created an answer with at least 3 up-votes. For A: ATAC-seq fragment length distribution
Scholar 7 months ago, created an answer that has been accepted. For A: ATAC-seq fragment length distribution
Popular Question 9 months ago, created a question with more than 1,000 views. For MeDIP-seq and hMeDIP-seq analysis
Great Question 10 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 2.2 years ago, created a question with more than 1,000 views. For MeDIP-seq and hMeDIP-seq analysis
Popular Question 2.3 years ago, created a question with more than 1,000 views. For MeDIP-seq and hMeDIP-seq analysis
Supporter 2.4 years ago, voted at least 25 times.
Popular Question 3.7 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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