User: writetoroopali

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Posts by writetoroopali

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Comment: C: Error while using buildindex for human genome
... Hi Wei, This is the output of fc$stat. > fc$stat                           Status 1                       Assigned 2            Unassigned_Unmapped 3      Unassigned_MappingQuality 4             Unassigned_Chimera 5      Unassigned_FragmentLength 6           Unassigned_Duplicate 7      ...
written 11 months ago by writetoroopali0
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Comment: C: Error while using buildindex for human genome
... Hi Wei, Thank you for your help so far. I am using the gapped index to do alignment and counting. Here's the code: fastq.files <- list.files(pattern = ".fastq.gz$", full.names = TRUE) buildindex(basename="GRCh37",reference="GRCh37_latest_genomic.fna",            gappedIndex=TRUE,indexSplit=TRUE ...
written 11 months ago by writetoroopali0
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Comment: C: Error while using buildindex for human genome
... Hi Wei,  Thank you so much for your response. I just have one more question: Does the one-block index or split index have impact on the number of assigned reads while using featureCounts? ...
written 11 months ago by writetoroopali0
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Comment: C: Error while using buildindex for human genome
... Hi Wei, When I use buildindex(basename="GRCh38",reference="GRCh38_latest_genomic.fna") I get: //=========================== indexBuilder setting ===========================\\ ||                Index name : GRCh38                        || ||               Index space : base-space                ...
written 11 months ago by writetoroopali0
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Comment: C: Error while using buildindex for human genome
... My R command is: buildindex(basename="GRCh38",reference="GRCh38_latest_genomic.fna") The reference genome sequence was downloaded from here: https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml   Thank you. Roopali   ...
written 11 months ago by writetoroopali0
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Comment: C: Error while using buildindex for human genome
... Hi Wei, Thank you so much for your reply. This is the sessionInfo for package "Rsubread": R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Fr ...
written 11 months ago by writetoroopali0
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Error while using buildindex for human genome
... Hi I am trying to do alignment and counting from a fastq file using package Rsubread. I am following the following instructions: http://combine-australia.github.io/RNAseq-R/07-rnaseq-day2.html However, every time I try to build index for the human genome the process is killed after 50% index is b ...
alignment rsubread fasta buildindex written 11 months ago by writetoroopali0

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