User: Morris_Chair

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Morris_Chair150
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Posts by Morris_Chair

<prev • 139 results • page 1 of 14 • next >
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GSEA and normalized reads count
... Hello everyone, I want to make a GSEA using the online tool of the Broad Institute. To do that I generally use FPKM or RPKM matrix and I was wondering if you think it's ok to use the normalized read file that I get as output from DESeq2 thank you ...
deseq2 rna-seq gsea written 18 days ago by Morris_Chair150
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Comment: C: convert MSTRG to human-readable format
... Hi Chahat, I handed up using a different pipeline for the RNA-seq analysis, sorry I can't help ...
written 18 days ago by Morris_Chair150
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Comment: C: IGV crashing on Mac
... I agree with ATpoint else, you could install a previous version of IGV ...
written 4 weeks ago by Morris_Chair150
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computeMatrix bed format files
... Hello everyone, I'm getting familiar with deeptools and I want to use the computeMatrix function. In the description it says: File name, in BED format, containing the regions to plot. If multiple bed files are given, each one is considered a group that can be plotted separately. what type of B ...
deeptools chip-seq written 4 weeks ago by Morris_Chair150
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Comment: C: (Galaxy) MACS2 peaks threshold
... yes in the picture is a bam, bamCoverage doesn't like my code and I have error, bamCoverage -bam SRR1104880.bam -binSize 10 -ignoreDuplicates -normalizeTo1x 2864785220 -fragmentLength 200 -o Coverage.SRR1104880.bw there is a conflict with Numpy :/ I see that galaxy has a similar function to ...
written 5 weeks ago by Morris_Chair150
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Comment: C: (Galaxy) MACS2 peaks threshold
... yes they validated with qPCR later, Thank you for your answer it helps :) ...
written 5 weeks ago by Morris_Chair150
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Comment: C: (Galaxy) MACS2 peaks threshold
... Hi ATpoint, in part I agree with you but I think that if it was input instead of IgG it would have been different, less background because reads are more randomly distributed (I guess). I adjusted the parameters as recommended on a galaxy tutorial that I found on youtube, do you think is it better t ...
written 5 weeks ago by Morris_Chair150
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(Galaxy) MACS2 peaks threshold
... Hello everyone, I am using galaxy to analyze ChIP-seq data downloaded from SRA. This team used as negative control the IgG and when I compare my genes of interest against the control using IGV I can visually see an enrichment of reads nearby the genes but MACS2 does't not recognize this peaks as ...
macs2 chip-seq written 5 weeks ago by Morris_Chair150
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Comment: C: MACS2 and single file for analysis
... I am doing things in parallel sorry for the confusion:D ok, I have only one file and I can still visualize significant peaks which is already good, I thought deeptools could run only with python, tnx ...
written 6 weeks ago by Morris_Chair150
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Comment: C: MACS2 and single file for analysis
... I read somewhere that when there is only one file MACS is able to apply a normalization in order to distinguish noise and peaks so it's not for this case. I will need to normalize against the input others files. yes it was a typo, I meant Rstudio tnx ...
written 6 weeks ago by Morris_Chair150

Latest awards to Morris_Chair

Popular Question 15 days ago, created a question with more than 1,000 views. For Bamfile first step analysis
Centurion 3 months ago, created 100 posts.
Supporter 7 months ago, voted at least 25 times.
Popular Question 8 months ago, created a question with more than 1,000 views. For Bamfile first step analysis

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