User: dimitrischat

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dimitrischat50
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Posts by dimitrischat

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Comment: C: gff file of constituent enhancer For Young algorithm
... H3K27Ac histone mod - Human (RPMI-8402) cells. Do i call them with macs2? I am sorry but obviously i am a newbie ...
written 6 weeks ago by dimitrischat50
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Comment: C: gff file of constituent enhancer For Young algorithm
... PURPOSE: To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff) input: files of sequencing reads for factor of interest and control i downloaded example data files to chec ...
written 6 weeks ago by dimitrischat50
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gff file of constituent enhancer For Young algorithm
... https://bitbucket.org/young_computation/rose/overview does anyone know where to find these enhancer gff files ? gff must have the following columns: 1: chromosome (chr#) 2: unique ID for each constituent enhancer region 4: start of constituent 5: end of constituent 7: strand (+,-,.) 9: unique ID ...
assembly written 6 weeks ago by dimitrischat50 • updated 7 days ago by Biostar ♦♦ 20
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rna seq - deseq2
... Hello all again, i was using cuffdiff (the last step) thus far to do rna-seq analysis but as i ve read and been told cuffdiff is outdated and now i have been using deseq2 ( i got no idea of R but with the help of this link : https://dwheelerau.com/2014/02/17/how-to-use-deseq2-to-analyse-rnaseq-data/ ...
rna-seq written 8 months ago by dimitrischat50 • updated 8 months ago by Biostar ♦♦ 20
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ftp server usegalaxy filezilla problem
... trying to connect with more than one pc/mac/linux but i cannot connect. account is ok and password ok. the error : Connecting to 129.114.60.60:21... Status: Connection established, waiting for welcome message... Status: Initializing TLS... Status: Verifying certificate... Stat ...
software error written 9 months ago by dimitrischat50 • updated 9 months ago by Devon Ryan82k
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Comment: C: RNA seq pipeline
... deseq2 and sleuth are both in R, right? is there any other program out there that doesnt need r? ...
written 9 months ago by dimitrischat50
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Comment: C: RNA seq pipeline
... Thank you for your reply. So what pipeline should i use? I have no idea with these programs. Also is hg38 complete? Someone told me that it isnt finished(?) yet? ...
written 9 months ago by dimitrischat50
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Comment: C: RNA seq pipeline
... thank you very much. What is the pipeline with those? I could really use your help. ...
written 9 months ago by dimitrischat50
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RNA seq pipeline
... Hello again. I am new to bioninformatics and i need some guidance. I am trying to do an RNA seq analysis but the output seems a bit wrong. I got a type of cells for example h at 0,3 and 6 hour, and i got 2 replicates. And i want to compare 0h to 3h and 0h to 6h. So my sampels are: h0b,h0c,h3b,h3c,h6 ...
rna-seq written 9 months ago by dimitrischat50
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tophat2 bowtie2index error
... hi all, trying to run tophat2 , with -G xx.gtf and bowtie2index. the command is : tophat2 --library-type fr-unstranded -g 1 -G /home/..../**Homo_sapiens.GRCh38.90.gtf** /home/..../Homo_sapiens/UCSC/hg38/Sequence/**Bowtie2Index/genome** /home/.../xx.fastq The error : Building Bowtie ind ...
rna-seq written 10 months ago by dimitrischat50 • updated 10 months ago by genomax54k

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Supporter 9 months ago, voted at least 25 times.

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