User: fabbri.marco

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Posts by fabbri.marco

<prev • 11 results • page 1 of 2 • next >
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Realignment disappeared in gatk4
... In GATK4 the indel realignment step will no longer be part of the pipeline. With my great surprise the tool has disappeared. My question, the algorithm is no more there because it doesn't improve the alignment? Do I need to search for a replace or should I just remove it from my pipeline since it is ...
gatk realignment written 4 weeks ago by fabbri.marco0 • updated 4 weeks ago by igor5.7k
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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 9 weeks 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 weeks 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 weeks 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 5 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 6 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 6 months ago by fabbri.marco0 • updated 6 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 6 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 9 months ago by fabbri.marco0 • updated 9 months ago by WouterDeCoster27k
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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 9 months ago by fabbri.marco0 • updated 9 months ago by Istvan Albert ♦♦ 76k

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