User: Konrad Rudolph

gravatar for Konrad Rudolph
Reputation:
130
Status:
New User
Location:
Cambridge, UK
Last seen:
6 years, 8 months ago
Joined:
7 years, 9 months ago
Email:
4***@biostars.org

PhD student in John Marioni’s group at EMBL-EBI in Cambridge.

Posts by Konrad Rudolph

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Difference Between Mapped And Unmapped Reads
... More efficient: samtools view -c -F0x4 aln_complete.sam ...
written 7.0 years ago by Konrad Rudolph130
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Comment: C: Converting Gff To Bed With Bedtools?
... OP wants the opposite. I.e. input GFF, output BED. ...
written 7.0 years ago by Konrad Rudolph130
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Answer: A: Annotation For Retrotransposons
... Answering my own question: Ensembl Biomart actually allows filtering by Gene type: “retrotransposed”. However, this only works in the current build of Ensembl and I am unfortunately forced to use an archived build since I’m working on the genome version NCBIM37. ...
written 7.2 years ago by Konrad Rudolph130
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Comment: C: Annotation For Retrotransposons
... Are LINEs and SINEs annotated in repeats though? Anyway, I’m gonna try this, thanks. ...
written 7.2 years ago by Konrad Rudolph130
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Annotation For Retrotransposons
... I’m searching for a downloadable annotation file for different types of ncRNA: in particular, rRNAs and retrotransposons for mouse. Most ncRNAs are not a problem – for instance, Ensembl provides a FASTA download of ncRNAs. Luckily, the actual sequence data is rather short and the file contains full ...
annotation rna ensembl written 7.2 years ago by Konrad Rudolph130 • updated 7.2 years ago by SES8.3k
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Comment: C: Macs 1.4 Reports Many Negative P-Values
... Right, I don’t know why I initially assumed p < 0. Of course p = 0 makes vastly more sense (but having the inclusive check in code is decidedly bad practice since it thus fails silently and masks bugs instead of alerting the user, and doesn’t state the intended semantic clearly). Be that as it ma ...
written 7.5 years ago by Konrad Rudolph130
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Macs 1.4 Reports Many Negative P-Values
... I am calling peaks on ChIP-seq data (BED files mapped with BWA) using MACS 1.4. I observed that there were a large number of peaks with a score of exactly 3100.00, while all the surroundings scores only belonged to single peaks. I did a bit of digging and discovered the following line of code in Pe ...
macs chip-seq peak-calling written 7.5 years ago by Konrad Rudolph130
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Answer: A: Convert Bowtie Output To Bwa
... In case anybody’s interested, this is the script I ended up using. Unfortunately, it’s **extremely** slow (I really cannot overstate that) and doesn’t parallelise. A better approach would be to use the `.bai` index file to collect all reads on a chromosome and run one job per chromosome in parallel. ...
written 7.6 years ago by Konrad Rudolph130 • updated 6 weeks ago by RamRS25k
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Comment: C: Convert Bowtie Output To Bwa
... @jingtao09 That’s effectively what I’m doing at the moment. ...
written 7.6 years ago by Konrad Rudolph130 • updated 6 weeks ago by RamRS25k
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Comment: C: Convert Bowtie Output To Bwa
... @jingtao09 I need it the other way round. :-( Furthermore, that script actually looks for an `XA` tag that contains the prefix `Z:` … I’m not sure what that is. It doesn’t seem to be the format I need though. ...
written 7.6 years ago by Konrad Rudolph130 • updated 6 weeks ago by RamRS25k

Latest awards to Konrad Rudolph

Supporter 6.7 years ago, voted at least 25 times.
Teacher 7.6 years ago, created an answer with at least 3 up-votes. For A: Convert Bowtie Output To Bwa

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