User: cg_ref_database

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Posts by cg_ref_database

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PureCN mappingbiasfile and minimum number of NormalDB samples question
... I am using the R-package PureCN to process predominantly tumor-only samples, but I do have 4 tumor-normal pairs. I understand that one processed matched normal sample (ideally derived from young and healthy individuals, sample processed using the same methods and probe kit as the tumor samples, sam ...
purecn question written 14 days ago by cg_ref_database20 • updated 13 days ago by markus.riester500
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Comment: C: PureCN Coverage.R error
... Yes, definitely, can I get the email account to send the BED file to? Also, just to be clear, is that the probes BED file? ...
written 4 weeks ago by cg_ref_database20
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Comment: C: PureCN Coverage.R error
... (continued) 2: In .Seqinfo.mergexy(x, y) : Each of the 2 combined objects has sequence levels not in the other: - in 'x': chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v ...
written 4 weeks ago by cg_ref_database20
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Comment: C: PureCN Coverage.R error
... The interval file command was: Rscript IntervalFile.R \ --infile Exome_v1_hg38_Probes_Standard_REMOVE_five.bed \ --fasta GRCh38.d1.vd1.fa \ --outfile ref_check_output/baits_hg38_intervals_hg38probes_grch38.d1.vdl.txt \ --offtarget --genome hg38 \ --export ref_check_output/ba ...
written 4 weeks ago by cg_ref_database20
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PureCN Coverage.R error
... I'm using the PureCN package to calculate GC-normalized coverage, but I'm receiving the following error below (bottom of page). After execution is halted, a compressed bed-type text file is produced that has intervals for each of the chromosomes: chr1:925918-926037 2150 25 1 0.880952380952381 ...
software error R next-gen tool written 4 weeks ago by cg_ref_database20 • updated 4 weeks ago by Istvan Albert ♦♦ 84k
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Comment: C: PureCN prepare environment error
... Thank you for the samtools command to check if there was something wrong with the fasta. The fasta was fine. The problem appears to be with the liftover (37 -> 38) of the probe.bed file. A comparison between the liftover bed-file and the probe.bed in hg38 coordinates (I was unaware that this f ...
written 5 weeks ago by cg_ref_database20
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Comment: C: PureCN prepare environment error
... Okay, the problem was with the GRCh38.d1.vd1.fa that I obtained from the cancer.gov website (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/#step-1-converting-bams-to-fastqs-with-biobambam-biobambam2-2054) and that I used to process my tumor-only samples w ...
written 5 weeks ago by cg_ref_database20
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Comment: C: PureCN prepare environment error
... My apologies, I still need assistance with the prepare environment step. Any help would be very much appreciated. The new error that I'm encountering now is: INFO [2020-07-07 01:07:10] Loading GCA_000001405.15_GRCh38_no_alt_analysis_set_100.bw... INFO [2020-07-07 01:08:04] Loading PureCN ...
written 5 weeks ago by cg_ref_database20
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Comment: C: PureCN prepare environment error
... The problem that I was encountering above was that the infile needed to be sorted, compressed and indexed: bedtools sort -i [infile] > [infile.sorted] bgzip -i [infile.sorted] ...
written 6 weeks ago by cg_ref_database20
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Comment: C: PureCN prepare environment error
... Thank you Markus, that was the problem for that part of the command. A new problem while still at the IntervalFile.R stage is that it gives the following error: [E::faidx_fetch_seq2] Failed to retrieve block. (Seeking in a compressed, .gzi unindexed, file?) Warning message: package 'optpars ...
written 6 weeks ago by cg_ref_database20

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