User: Bogdan

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Bogdan1.1k
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Posts by Bogdan

<prev • 318 results • page 1 of 32 • next >
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HI-C analysis in the cloud environment
... Dear all, does anyone know a HI-C analysis pipeline available in the cloud environment ? thanks a lot, bogdan ...
hi-c written 2 days ago by Bogdan1.1k
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CUT&TAG and CUT&RUN
... Dear all, referring to CUT&TAG and CUT&RUN techniques, i was wondering if someone has been already working on these techniques, and more specifically : -- if the standard peak callers in ChIP-seq (HOMER, SICER, MACS2) would be well-accepted (from a statistical point of view) on CUT&T ...
chip-seq written 4 weeks ago by Bogdan1.1k • updated 4 weeks ago by i.sudbery11k
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Comment: C: scRNA-seq, MONOCLE3, and trajectory reconstruction, and Moran I statistics
... Hi : i 'd think that one way would be to filter based on the number of counts per GENE at the beginning and end of the trajectory; i have started to look a while ago into TradeSeq (https://github.com/statOmics/tradeSeq) that has good documentation :) ...
written 6 weeks ago by Bogdan1.1k
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Comment: C: recent Hi-C databases
... thanks a lot, very very helpful ! ...
written 7 weeks ago by Bogdan1.1k
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recent Hi-C databases
... Dear all, please would you let me know if there are any Hi-C databases that would have collected the 3C interactions reported by individual laboratories, or big consortia such as ENCODE or 4Dnucleome ? thanks a lot, -- bogdan ...
hi-c 4c 3c written 7 weeks ago by Bogdan1.1k • updated 7 weeks ago by jared.andrews078.6k
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Comment: C: visualize RNA secondary/tertiary structure, and overlay the primary sequence
... many many thanks, Mensur ! the field is still new to me, and many thanks for all your help and articles that you have pointed it :) I have been asking the question in the context of the biological question "how mRNAs localized in the axons ?" (based on Ribo-trap method (https://www.ncbi.nlm.nih.gov/ ...
written 10 weeks ago by Bogdan1.1k
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Comment: C: visualize RNA secondary/tertiary structure, and overlay the primary sequence
... thanks a lot, Mensur for a very detailed and insightful reply. If i may add please : shall we compare : a) the MFE (or Z-scores) of overlapping windows along the full-length mRNAs with b) the MFE (or Z-scores) of overlapping windows of random synthetic RNA sequences would you expect to see lar ...
written 10 weeks ago by Bogdan1.1k
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Comment: C: visualize RNA secondary/tertiary structure, and overlay the primary sequence
... Thanks a lot, Mensur. Yes, it is a great app, very intuitive and easy to use. Thanks ! i have been exploring also Chimera from UCSF : https://www.cgl.ucsf.edu/chimera/ on another note, if I may ask please : how much secondary shall we see in mRNAs ? As they get exported to cytosol, and translated ...
written 10 weeks ago by Bogdan1.1k
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visualize RNA secondary/tertiary structure, and overlay the primary sequence
... Dear all, please may i ask : which software would you recommend for the visualization of the RNA secondary / tertiary structure (available in the PDB files), and overlay the primary sequence (or other annotations). thanks a lot, with much appreciation ! -- bogdan ...
rna rna structure visualization written 10 weeks ago by Bogdan1.1k
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Comment: C: filtering the somatic variants
... we can search the latest publications on pubmed please. Recently, i've been doing mainly scRNA-seq analyses. ...
written 11 weeks ago by Bogdan1.1k

Latest awards to Bogdan

Popular Question 28 days ago, created a question with more than 1,000 views. For mutation detection in tumors samples
Great Question 4 weeks ago, created a question with more than 5,000 views. For intersect VCF files
Great Question 5 weeks ago, created a question with more than 5,000 views. For intersect VCF files
Epic Question 6 weeks ago, created a question with more than 10,000 views. For intersect VCF files
Popular Question 6 weeks ago, created a question with more than 1,000 views. For mutation detection in tumors samples
Popular Question 8 weeks ago, created a question with more than 1,000 views. For mutation detection in tumors samples
Popular Question 12 weeks ago, created a question with more than 1,000 views. For about GATK VariantAnnotator and VCF files
Great Question 3 months ago, created a question with more than 5,000 views. For intersect VCF files
Student 3 months ago, asked a question with at least 3 up-votes. For single cell RNA-seq pipeline
Popular Question 3 months ago, created a question with more than 1,000 views. For mutation detection in tumors samples
Popular Question 3 months ago, created a question with more than 1,000 views. For mutation detection in tumors samples
Popular Question 5 months ago, created a question with more than 1,000 views. For running GATK or Mutect or a somatic variant caller individual chromosomes
Popular Question 5 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Popular Question 5 months ago, created a question with more than 1,000 views. For SAM file and RNA-seq stranded/unstranded paired/unpaired
Popular Question 5 months ago, created a question with more than 1,000 views. For linking GATK to MUTECT
Popular Question 5 months ago, created a question with more than 1,000 views. For mutation detection in tumors samples
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Single Cell RNA Seq. Analysis
Popular Question 7 months ago, created a question with more than 1,000 views. For SAM file and RNA-seq stranded/unstranded paired/unpaired
Popular Question 7 months ago, created a question with more than 1,000 views. For running GATK or Mutect or a somatic variant caller individual chromosomes
Popular Question 7 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Popular Question 10 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Popular Question 10 months ago, created a question with more than 1,000 views. For SAM file and RNA-seq stranded/unstranded paired/unpaired
Popular Question 10 months ago, created a question with more than 1,000 views. For running GATK or Mutect or a somatic variant caller individual chromosomes
Guru 11 months ago, received more than 100 upvotes.
Student 11 months ago, asked a question with at least 3 up-votes. For filtering the somatic variants

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