User: Roman Hillje

gravatar for Roman Hillje
Roman Hillje40
Reputation:
40
Status:
New User
Location:
Milan, Italy
Last seen:
3 weeks, 5 days ago
Joined:
4 years, 3 months ago
Email:
r***********@googlemail.com

Posts by Roman Hillje

<prev • 33 results • page 1 of 4 • next >
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Comment: C: Merge several bigWig files (with different intervals) into single GRanges object
... Thanks for the suggestion, I'll look into that in a bit more detail tomorrow. Perhaps I should mention, however, that I'll be working on at least 16 profiles (in groups of 4), and ideally 108 profiles in total. It's no problem at all to plot them as separate tracks (actually I'm impressed by how fas ...
written 26 days ago by Roman Hillje40
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Merge several bigWig files (with different intervals) into single GRanges object
... Hi everybody, I've been banging my head against the wall for a few hours and finally decided to ask for some help here. What I need to do is relatively straight-forward: I have a number of bigWig files, which were generated by deepTools and belong to two experiments groups, that I would like to pl ...
R genomicfeatures gviz chip-seq rtracklayer written 27 days ago by Roman Hillje40 • updated 26 days ago by noshadho0
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Comment: C: Downloading paired end fastq from SRA
... While the results I got indicated serious issues in some samples according to Cell Ranger (few reads in cells), it did work as expected. That is, you download the BAM, re-generate the FASTQ files from the using the bamtofastq tool posted by Igor, and use that as input to Cell Ranger. I couldn't find ...
written 10 months ago by Roman Hillje40
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Comment: C: Downloading paired end fastq from SRA
... Thank you for the link. I didn't know about that tool. I will test it with the BAM files provided by the authors and, if I remember, report back if I was successful. ...
written 10 months ago by Roman Hillje40
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Comment: C: Downloading paired end fastq from SRA
... You can find the R2 (100bp) in the SRA and can download it from there (https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR6860519). Which is what I did and then found out that's all there is... And the BAM file (output of Cell Ranger) is pretty useless if they don't also upload the transcript count m ...
written 10 months ago by Roman Hillje40
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Comment: A: Downloading paired end fastq from SRA
... I know this is old but I came across this thread because I had problems downloading paired-end data from SRA as well (getting only one file even though protocol says it was paired). Only after reading the description I realized it is the exact same data set I tried to access. I'll just use this oppo ...
written 10 months ago by Roman Hillje40
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Taking scores from DiffBind for other analysis?
... Hi guys, Can anybody tell me if it's legitimate to extract the `Score` values from the DiffBind analysis and use them for down-stream analysis? Let's say I want to do GSEA with the H3K4me3 signal in all TSS regions. Could I take the `Score` column (which you find directly before the `RPKM` column)? ...
diffbind chip-seq written 20 months ago by Roman Hillje40
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Get positions in BAM with reads supporting at least 2 different nucleotides
... Hi guys, I'm currently looking for a tool or script that takes a BAM file (from an RNAseq experiment) and outputs a list of all the positions that have reads supporting at least 2 different nucleotids (WT vs variant or whatever you want to call it). Ideally, it also reports the coverage so I can fi ...
rna-seq written 22 months ago by Roman Hillje40 • updated 22 months ago by Pierre Lindenbaum129k
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Comment: C: List of TSS from GTF file
... Thanks, I don't know how I missed this obvious step. That brought the list down to a manageable number (~50k). And taking the `start`/`end` for `+`/`-` strand, respectively, is the right way to go? ...
written 2.3 years ago by Roman Hillje40
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List of TSS from GTF file
... Hi, I'd like to create lists of transcription start sites based on the GTF files of the multiple annotation sets we have in our group. For example, for mm10 we have GENCODE annotation, RefSeq annotation, refGene etc. For each of them, I have a GTF/GFF file. Having a list of TSS regions is particula ...
gtf tss written 2.3 years ago by Roman Hillje40 • updated 2.3 years ago by Alex Reynolds30k

Latest awards to Roman Hillje

Popular Question 10 months ago, created a question with more than 1,000 views. For List of TSS from GTF file
Popular Question 10 months ago, created a question with more than 1,000 views. For Analysis of BAF from SNP array data
Popular Question 10 months ago, created a question with more than 1,000 views. For Extract further information from deepTools plotPCA
Popular Question 10 months ago, created a question with more than 1,000 views. For Comparison of ChIPseq enrichment in specific regions
Popular Question 20 months ago, created a question with more than 1,000 views. For Analysis of BAF from SNP array data
Popular Question 20 months ago, created a question with more than 1,000 views. For Extract further information from deepTools plotPCA
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Analysis of BAF from SNP array data

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