User: rob.costa1234

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rob.costa1234250
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Posts by rob.costa1234

<prev • 160 results • page 1 of 16 • next >
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Trimmomatic trimming 3' bases
... I want to trim 3' - 20 bases of FASTq in PE file but could not figure out the option @ http://www.usadellab.org/cms/index.php?page=trimmomatic Any pointer will be highly appreciated. Thanks ...
sequence written 8 days ago by rob.costa1234250 • updated 7 days ago by shelkmike290
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annotation of chipseq peaks
... I have a Chipseq data with peak coordinates that I want to overlay with 3 public data sets associated with the same protein. I have used bed tools to intersect coordinates to check the overlap of my data with public datasets. I was wondering if it is reasonable do the Go/ pathway analysis with peaks ...
chip-seq written 11 days ago by rob.costa1234250
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Comment: A: sequencing depth in ScRNASeq
... Though it is an old thread but question seems to be relvant I ran 10x samples in MiSeq and estimated cells around 2000. However, Miseq suggest around 50 cells per sample. QC of FASTA files is good. If the sequencing is done on nova seq. or another sequencer -next seq will it capture more cells? Does ...
written 25 days ago by rob.costa1234250
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(Closed) Starsolo is not extracting barcodes
... On10X data (ScRNA) and am trying to run Starsolo, however it is not extracting barcodes from sequencing file. What may be the reason. I have used all the parameters as suggested @ https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/scrna-preprocessing-tenx/tutorial.htm ...
rna-seq written 4 weeks ago by rob.costa1234250
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Fasta file from Gencode
... If I have to use gff3 file of gencode as gene model (gencode.v35.annotation.gff3.gz ) which Fasta file should be used for alignment from https://www.gencodegenes.org/human/ as summarized in image below https://ibb.co/SmfYqNz ...
sequence alignment written 4 weeks ago by rob.costa1234250 • updated 4 weeks ago by genomax91k
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3D structures of compounds
... Is there a a database to search 3D structure of chemicals/ small molecules that can be drugs or inhibitor of disease progression ...
drugs database peptides written 8 weeks ago by rob.costa1234250 • updated 7 weeks ago by Biostar ♦♦ 20
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Comment: A: Cell type pathway ScRNAseq
... I am also interested to know what pathway tool is used for single cell RNA seq data. ...
written 4 months ago by rob.costa1234250
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pathway genes for mouse
... I am looking for list of genes associated with EGF pathway of mouse. Is there a database or other method to access such list. Msig, David and other don't provide such list but will analyze list of genes ...
pathway written 6 months ago by rob.costa1234250 • updated 6 months ago by Jean-Karim Heriche23k
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Comment: A: microRNA-seq analysis from RNA-seq data
... You will be better of doing small RNA seq separately to analyze micro or other small RNA ...
written 6 months ago by rob.costa1234250
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Comment: C: Question about COVID19 data sets
... It is useful. I think it does not have clinical out come of patients as well as hosts sequencing as noted in second point. ...
written 6 months ago by rob.costa1234250

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