User: thefirstrealace

Reputation:
30
Status:
New User
Location:
Germany
Last seen:
3 years, 2 months ago
Joined:
3 years, 12 months ago
Email:
t**************@gmail.com

Posts by thefirstrealace

<prev • 29 results • page 2 of 3 • next >
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Calculate binned methylation data throughout hg19 with BEDOPS
... Hello, i need to digitize DNA methylation data througout the whole hg19. To be more precise, i need to generate smoothed density signal by binning the genome into 20 bp intervals and then run a sliding window over the whole genome. I already downloaded the methylation data as a BED file and i have ...
bedops methylation data hg19 written 3.7 years ago by thefirstrealace30 • updated 3.5 years ago by Shicheng Guo7.8k
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Comment: C: Need help with statistics: Quartiles and Median
... Thank you very much, that was very helpful ...
written 3.7 years ago by thefirstrealace30
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Comment: C: Need help with statistics: Quartiles and Median
... I actually use R, but im still new to it. If is understand correctly, rm.na=TRUE filters out the NA and only uses the remaining data points for the calculation of quartiles and median? ...
written 3.7 years ago by thefirstrealace30
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Need help with statistics: Quartiles and Median
... Hello everybody, i need some help with statistical anylsis of biological properties. Assume, that for some biological properties A, B, C and D, we have their occurence given as m/n-ratios. We have these data for three example species S1 to S3 in a table like shown below (My real data set contains 1 ...
median quartile statistics written 3.7 years ago by thefirstrealace30 • updated 3.7 years ago by RamRS24k
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Answer: A: Biopython script to change file formats and headers
... Hello, your second code block looks a little bit weird to me, normally you need to define a file handle for the SeqIO parser like shown below: handle = open(labels[0] + ".fasta", "rU") for seq_record in SeqIO.parse(handle, "fasta"): seq_record.id = labels[0] # renaming the pseudogene with ...
written 3.8 years ago by thefirstrealace30
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How to get Cufflinks data for MISO alternative splicing events?
... Hello, i am currently doing an analysis on splice junctions at alternative exons, that belong to exon-skipping (ES) events. Therefore i have done the following steps so far: I downloaded mRNA-Seq reads from human spleen cells from GEO I used TopHat to mao these reads to hg19 I used TopHats acc ...
tss fpkm cufflinks ensembl annotation miso written 3.8 years ago by thefirstrealace30 • updated 3.7 years ago by Biostar ♦♦ 20
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Comment: C: TSS / TTS in Ensembl gene annotation?
... Thank you very much for your help, for some reason I never considered the cDNA features in this file, but it actually makes perfect sense :) ...
written 3.8 years ago by thefirstrealace30
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TSS / TTS in Ensembl gene annotation?
... Hello, i have one question about a gene annotation i downloaded recently in gff3 format. Below is an abreviated example containing the first few lines of this file: ##gff-version 3 # Generated on Tue Nov 27 19:25:49 2012 # UCSC table file ./ucsc_tables/hg19/ensGene.txt chr1    ensGene    gene     ...
ensembl gff gene annotation written 3.8 years ago by thefirstrealace30 • updated 3.8 years ago by Emily_Ensembl19k
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Confusing values in MISO output file
... Hello, i have the following problem. I first used TopHat to map my RNA-Seq reads to the hg19 reference. After that i used TopHat's accepted_hits.bam file to search for alternative splicing events with MISO. I did everything like it was described in the MISO manual and everything was fine (No errors ...
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Comment: C: How to analyze methylation around splice junctions
... Hi, the workflow actually turns out to be very simple, but depending on your hardware it might be very time-consuming. I did the following steps: Download RNA-Seq data in SRA-format from GEO (i took data from spleen) Extract reads with the SRA toolkit (take care of library type!!! single-end or ...
written 3.8 years ago by thefirstrealace30

Latest awards to thefirstrealace

Scholar 3.9 years ago, created an answer that has been accepted. For A: Ubuntu: MISO unittest fails

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