User: salamandra

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salamandra130
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Posts by salamandra

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Comment: C: RNA-seq: Should remove duplicates in all samples of same experiment although som
... yes, but then i read the link you had [provided][1] and understood that at least for the samples where the duplication level vs reads per kilobase graph was 'ugly' we could infer most of the duplicates were technical. And as some of my samples had those 'ugly' graphs i had the question whether we c ...
written 7 days ago by salamandra130
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RNA-seq: Should remove duplicates in all samples of same experiment although some do not have technical duplicates?
... 1- The graph of % duplication vs read coverage of RNA-seq [sample 1][1] seems to have technical duplicates, but can we say the same for [sample 2][2] and [sample 3][3]? 2- If we remove duplicates in one sample (because the graph % duplication vs read coverage suggests there's technical duplicate ...
dupradar rna-seq duplication written 7 days ago by salamandra130
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Comment: C: Mark duplicates PICARD error: Unable to access jarfile 'MarkDuplicates.jar' with
... the file was there, it was missing $. no need to be rude... thank you for your help ...
written 13 days ago by salamandra130
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Comment: C: Mark duplicates PICARD error: Unable to access jarfile 'MarkDuplicates.jar' with
... p.s. you suggested v2.19, but i don't know how to install 2.19 with Anaconda (I used `conda install -c bioconda picard` to update to v2.18 ...
written 13 days ago by salamandra130
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Comment: C: Mark duplicates PICARD error: Unable to access jarfile 'MarkDuplicates.jar' with
... Now with picard 2.18 I run this: BAM_file=/Volumes/PereiraLab/Tania/RNAseqcourse/material/results/results_fastqexamples/alignments/HISAT2_adapter_removed_qualitytrim_20150821.A-2_BGVR_P218_R1_paired_with_retrievedgenome_ensembl.bam output=/Volumes/PereiraLab/Tania/RNAseqcourse/material/resu ...
written 13 days ago by salamandra130
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Comment: C: Mark duplicates PICARD error: Unable to access jarfile 'MarkDuplicates.jar' with
... when providing full path to picard. jar file: java -jar /Applications/Anaconda/pkgs/qualimap-2.2.2a-2/share/qualimap-2.2.2a-2/picard-1.70.jar -h still gives error: no main manifest attribute, in /Applications/Anaconda/pkgs/qualimap-2.2.2a-2/share/qualimap-2.2.2a-2/picard-1.70.jar ...
written 13 days ago by salamandra130
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Comment: C: Mark duplicates PICARD error: Unable to access jarfile 'MarkDuplicates.jar' with
... right. I though it was PICARD's help menu but it's java help menu. So I have to write the path to the picard.jar file is that it? ...
written 13 days ago by salamandra130
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Comment: C: Mark duplicates PICARD error: Unable to access jarfile 'MarkDuplicates.jar' with
... it's this: java -jar -h java -jar MarkDuplicates ...
written 13 days ago by salamandra130
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Comment: C: Mark duplicates PICARD error: Unable to access jarfile 'MarkDuplicates.jar' with
... in Rstudio any doesn't work with or without quotes ...
written 13 days ago by salamandra130
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Comment: C: Mark duplicates PICARD error: Unable to access jarfile 'MarkDuplicates.jar' with
... by doing on commandline: java -jar $PICARD -h it prints an output, but with: java -jar $PICARD MarkDuplicates gives error: Error: Unable to access jarfile MarkDuplicates ...
written 13 days ago by salamandra130

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