User: Grinch

gravatar for Grinch
Grinch30
Reputation:
30
Status:
New User
Location:
Germany
Last seen:
3 hours ago
Joined:
3 years, 8 months ago
Email:
s**********@gmail.com

Posts by Grinch

<prev • 23 results • page 1 of 3 • next >
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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 25 days ago by Grinch30
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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 6 months ago by Grinch30
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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 6 months ago by Grinch30
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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 6 months ago by Grinch30 • updated 5 months ago by EagleEye6.2k
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Comment: C: ATAC-seq fragment length distribution
... I've added the information in the description. ...
written 7 months ago by Grinch30
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Comment: C: ATAC-seq fragment length distribution
... I've added the information in the description. ...
written 7 months ago by Grinch30
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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 7 months ago by Grinch30
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Comment: C: samtools idxstats reports zero aligned or unaligned reads
... Bowtie output doesn't give the number of mapped reads per chromosome. I'm actually trying to replicate the data from an article and they claim they have used Bowtie2 for the alignment and after that, they have a script on GitHub which automates the downstream processing. But the script doesn't work ...
written 12 months ago by Grinch30
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Comment: C: samtools idxstats reports zero aligned or unaligned reads
... The index was made yesterday and I have also tried re-doing the conversion sam to bam, sorting, and indexing. With samtools view command, i get the number of mapped reads so everything is correct, but still idxstats doesn't want to give me any reads. ...
written 12 months ago by Grinch30
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samtools idxstats reports zero aligned or unaligned reads
... I've aligned ChIP-seq data that is publically available (SRP004897), with Bowtie2 -k 3 command. I need information on the number of aligned reads per chromosome for downstream processing, for which I've used samtools idxstats. The output of idxstats shows 0 aligned and 0 unaligned reads, see below: ...
idxstats samtools written 12 months ago by Grinch30 • updated 10 months ago by Biostar ♦♦ 20

Latest awards to Grinch

Popular Question 13 days ago, created a question with more than 1,000 views. For MeDIP-seq and hMeDIP-seq analysis
Great Question 8 weeks 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 18 months ago, created a question with more than 1,000 views. For MeDIP-seq and hMeDIP-seq analysis
Popular Question 19 months ago, created a question with more than 1,000 views. For MeDIP-seq and hMeDIP-seq analysis
Supporter 19 months ago, voted at least 25 times.
Popular Question 3.0 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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