User: rcaloger

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rcaloger500
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Posts by rcaloger

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News: An introductory course to RNA-seq 17-19 March 2015
... The Bioinformatics & genomics unit at Molecular Biotechnology Center (Torino, Italy) organizes an introductory course on RNAseq on 17-19 March 2015 This hands on course is suitable for biologists who are new to RNA-seq technology. This workshop will enable to gather information on the critical ...
news course rna-seq written 4.2 years ago by rcaloger500
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Answer: A: Single end STAR Chimeric.out.junction fails to read with chimera::importFusionDa
... I think the problem is related to the version of the human genome you have used. Are you using hg38? In the actual stable version it only allow the use of hg19. This issue is solved in the devel version. Could please try to use the devel version? If the problem is not solved with the devel could ...
written 4.3 years ago by rcaloger500
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Answer: A: Problem Importing STAR fusion data into chimera
...   Hi Angela, It seems that some of the detected sequences involved in the fusion cannot be extracted from the human genome present in bioconductor. Which genome version did you used for STAR mapping? It is important that chimera version of genome and the one used for the mapping are the same. In ...
written 4.5 years ago by rcaloger500
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Comment: C: Extracting protein sequence associated to UCSC transcript id
... Great! Thanks Raf On 09/01/14 15:19, James W. MacDonald wrote: > Hi Raf, > > The GenomicFeatures vignette covers these packages: > > http://www.bioconductor.org/packages/release/bioc/vignettes/GenomicF eatures/inst/doc/GenomicFeatures.pdf > > > Best, > > Jim > > ...
written 5.4 years ago by rcaloger500
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Extracting protein sequence associated to UCSC transcript id
... Hi, In order to validate fusion products I need to be sure that the peptides encoded by the the two fused proteins are in the same frame. I have now a function that allows to confirm the protein1 and protein2 have sequences located in the same frame. However, I got stack to retrieve those proteins s ...
written 5.4 years ago by rcaloger500 • updated 5.4 years ago by Michael Lawrence11k
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about coverage profile comparison
... Hi, I am investigating the interplay of different isoforms, in alternative splicing differential expression. I would like to compare coverage profiles of the same isoform with or without the presence of the other isoforms, there is any tool, in bioconductor, that allows manipulation of coverage prof ...
coverage written 5.7 years ago by rcaloger500 • updated 5.7 years ago by Wolfgang Huber13k
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filterBam
... Hi, I am trying to filter a bam file using a set of coordinates. I sorted the bam file using both sortBam or Picard SortSam tools but I always get the same error: filterBam("accepted_hits.sorted.bam", "accepted_hits.tp_exons", param=ScanBamParam(which=exons.gr)) Error in FUN("/data03/calogero/Docu ...
alignment written 5.8 years ago by rcaloger500 • updated 5.8 years ago by raffaele calogero500
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Answer: A: Annotation of Human Exon 1.0 ST
... I wonder if an annotation package used by oneChannelGUI could be useful to you. The packages: HuExExonProbesetLocation,MoExExonProbesetLocation andRaExExonProbesetLocation are derived by Affymetrix data annotation and contains the following info: library(HuExExonProbesetLocation) as.data.frame(HuE ...
written 6.0 years ago by rcaloger500
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filterBam using rname
... I have the necessity to filter a Bam file, keeping only reads associated to a subset of references. I wanted to do it with filterBam (Rsamtools) but I could not manage to find a way of doing it. If I use the code: filterBam("onlymapped.bam", "filtered.bam", param=ScanBamParam(which=my.rnames, what= ...
written 6.6 years ago by rcaloger500 • updated 6.6 years ago by Valerie Obenchain6.7k
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Comment: C: problem in reading bam files with EDASeq
... Many thanks for the nice comment I will definetively try this functionality of Rsamtools. Concerning the problem I had with EDASeq, I solved Filtering with Rsamtools the bam file: removing all unmapped and unpaired PE reads. This bam filtered file works perfectly on EDASeq cheers Raffaele Sent from ...
written 7.3 years ago by rcaloger500

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