User: Roman Hillje

gravatar for Roman Hillje
Roman Hillje30
Reputation:
30
Status:
New User
Location:
Milan, Italy
Last seen:
5 months, 1 week ago
Joined:
3 years, 1 month ago
Email:
r***********@googlemail.com

Posts by Roman Hillje

<prev • 27 results • page 1 of 3 • next >
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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 5 months ago by Roman Hillje30
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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 7 months ago by Roman Hillje30 • updated 7 months ago by Pierre Lindenbaum120k
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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 13 months ago by Roman Hillje30
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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 13 months ago by Roman Hillje30 • updated 13 months ago by Alex Reynolds28k
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Merging multiple scRNAseq samples: Normalize first and then merge or merge and normalize all together?
... Hi, I was hoping you guys could give me some advice on single-cell RNAseq analysis. I have four samples that belong to the same experiment. They were generated with the 10X Chromium (DropSeq) technology but I'd like to do the analysis independent from their software. Currently, this workflow is bas ...
scrnaseq written 16 months ago by Roman Hillje30
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Answer: A: ChromHMM Output Descriptions
... I'm currently studying how ChromHMM produces its output with a particular interest in the relationship between the enrichment values found in the `_overlap.txt` file and the colors in the heatmap (since I need to reproduce them). I went through the ChromHMM code and found that the heatmap is produce ...
written 18 months ago by Roman Hillje30
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Comment: C: Extract specific nucleotide AND total read information (tags) from BAM
... Hey Pierre! Sorry to bother you again but I was wondering if it's possible to modify the script so that it also outputs reads that have a deletion in the given position? I've been spending some time trying to figure it out myself but haven't been able to. Best would be if it could write something li ...
written 18 months ago by Roman Hillje30
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Comment: C: Extract specific nucleotide AND total read information (tags) from BAM
... Just tested it and this is exactly what I needed. Thank you so much! ...
written 18 months ago by Roman Hillje30
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Comment: C: Extract specific nucleotide AND total read information (tags) from BAM
... Again, sorry, could've made it a bit more clear. Some of the reads in my BAM file are cut in pieces with one piece aligning before the position of interest and the other piece after the position of interest. The CIGAR string then looks like this: 12M1441N39M. `samtools view` also reports these reads ...
written 18 months ago by Roman Hillje30
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Comment: C: Extract specific nucleotide AND total read information (tags) from BAM
... My bad, done! Don't know why I didn't do it before. ...
written 18 months ago by Roman Hillje30

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Popular Question 16 months ago, created a question with more than 1,000 views. For Analysis of BAF from SNP array data

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