User: fabbri.marco

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Posts by fabbri.marco

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Comment: C: varscan2 somatic sip
... Yes the sounds reasonable, I have to check the settings in varscan. Probably I have to allow to define Germaine above a percentage or number of reads. Any suggestions? ...
written 8 days ago by fabbri.marco0
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Comment: A: varscan2 somatic sip
... I think that I will change my setting, since this is in my opinion is a somatic mutation, there only 2 reads in the normal sample (lymphoma). I check how to set varscan option in a way that this should be predicted as somatic. What do you think? Marco ...
written 9 days ago by fabbri.marco0
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varscan2 somatic sip
... I have used varscan2 and the results below are not clear to me.I compared a tumour to a normal and I am interested in somatic mutation. The following snp is predicted as germline and I expected as somatic but it is not clear to me the reason, Any suggestions? Thanks Marco ##fileformat=VCFv4.1 ...
somatic varscan2 snp written 9 days ago by fabbri.marco0
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problem to filter freq from vcf produced with varscan
... I have a VCF file obtained from the Varscan2 tool. I want to filter the variants based on "FREQ". I used SnpSift (SnpSiftVersion="SnpSift 4.2 (build 2015-12-05), by Pablo Cingolani"). When I used the command: java -Xmx64g -jar ${SNPSIFT_JAR} extractFields $svcf "GEN[1].FREQ" I got the right fie ...
vcf filter varscan2 snpsift written 3 months ago by fabbri.marco0
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nanopore-Illumina hybrid RNA assembly
... I am planning to run nanopore-Illumina hybrid assembly. I work with plant. I have run some RNA sequencing with Illumina and some with nanopore. I read that with rnaspdes is possible to assemble Illumina and nanopore fastq in the same run. Any suggestions or comments? Thank you Marco ...
rna nanopore-illumina hybrid assembly written 4 months ago by fabbri.marco0
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Help with microarray annotation
... Dear all, I have received a tab separated file with probeset and thre column with gene expression. This matrix comes out from from old microarray study with SurePrint G3 Mouse Gene Expression v2 8x60K Microarray. I would like to add two extra column with gene annotation: GENE_ID and gene name. any ...
annotation sureprint microarray mouse written 4 months ago by fabbri.marco0 • updated 4 months ago by Shervin Alaei0
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Alignment of exome to gene set
... I was asked to reanalyse exome data (illumina DNA) I am interested only to 50 genes. Can I limit the allignement to the genes of interest ? Since the samples are 400, I would like to save time. Thanks Marco ...
alignment sequencing written 4 months ago by fabbri.marco0
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number reads fastq
... I am analysing a cancer panel. I am looking atf a number of reads for each fastq in the same flowcells. I have seen a difference in the number od reads when I have to start to worry? below tthe table: file num reads percentage 1_S1_L001_R1_001.fastq.gz 1001223 2.58924706156174 1_S1_L001 ...
fastq written 7 months ago by fabbri.marco0 • updated 7 months ago by WouterDeCoster26k
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Human Breast Cancer Panel QIAseq manifest
... I am looking for the manifest file for QIAsq Human Breast Cancer Panel DHS-001Z. I google for it but I could not find it. Any suggestion? thanks Marco ...
panel job manifest written 7 months ago by fabbri.marco0 • updated 7 months ago by Istvan Albert ♦♦ 75k
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intersect snp and exon coordinates
... I intersected exon coordinates with coordinates of mutations and I get the bed file with exons that contain mutations. This can be done with bedtools. I would like to do a little bit more articulates, I would like to do the same but select only exons that intersect with two mutations. Any suggesti ...
sequence snp written 13 months ago by fabbri.marco0 • updated 13 months ago by geek_y8.2k

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