User: micro32uvas

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Posts by micro32uvas

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Comment: C: Validation in paired end data alignment
... I doubt that, I got paired end data, mapped both reads with 99.14% coverage. Here's the flagstat of he data 253528473 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 251345729 + 0 mapped (99.14%:-nan%) 253528473 + 0 paired in sequencing 126740748 + 0 read1 ...
written 10 weeks ago by micro32uvas0
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Validation in paired end data alignment
... Hello Everyone! I am dealing with whole genome reseq data from Illumina platform for paired end data. Here's the flow,I've been following: 1. Fastq-->Sam (BWA mem with -M switch) 2. Sam-->Bam (Samtools view -b -S with F-2308 switch, which just didnt worked out for mate pairs, so i shifted ...
picard alignment samtools view -f2304 written 10 weeks ago by micro32uvas0
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Comment: C: RealignerTargetCreator inputs multiple Bams??
... i cannot understand how would this omit realignment. wouldn't realigner give further improvement in terms of mapping and enhanced calibration. If you could precisely share the command that would cover all of it, it would be highly appreciated ...
written 12 weeks ago by micro32uvas0
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Comment: C: RealignerTargetCreator inputs multiple Bams??
... Can you kindly elaborate this Devon? Actually i am working on Haplotypecaller but along with this preprocessing phase. i.e. after marking duplicates, now i am up with realign target creator, indel realigner and then base calibration. Then would be the haplotype calling using haplotype caller. Your ...
written 12 weeks ago by micro32uvas0
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Comment: C: RealignerTargetCreator inputs multiple Bams??
... You just solved my problem Pearl :) I'll get back here, if there's still some errors ...
written 12 weeks ago by micro32uvas0
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Comment: C: RealignerTargetCreator inputs multiple Bams??
... I never prefer Galaxy anyways, and yes its very limited as well. Its just I was missing the -I switch everytime, which was creating the problem. I just checked in galaxy for the given options there, if i was missing any. Thanks Devon ...
written 12 weeks ago by micro32uvas0
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RealignerTargetCreator inputs multiple Bams??
... Hello Everyone, I have been working with RealignerTargetCreator and in its pages, [RealignerTargetCreator][1]. It states that it takes multiple inputs as Bam. But its not taking it. when I checked Galaxy.it stated that GenomeAnalysisTK: RealignerTargetCreator accepts **an** aligned BAM input file. ...
gatk bam realignertargetcreator written 3 months ago by micro32uvas0 • updated 3 months ago by Devon Ryan69k
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Comment: C: Is my file created completely
... **bwa mem -t 48 genome.fa reads.fastq | samtools sort -@ 20 -O BAM -o output.bam -** It didnt work, following are the errors: sort: invalid option -- 'O' open: No such file or directory [bam_sort_core] fail to open file BAM [M::bwa_idx_load_from_disk] read 0 ALT contigs ...
written 3 months ago by micro32uvas0
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Comment: C: Is my file created completely
... No viewing? no samtools view command? In that case we are not indexing either. Additionally the bam created here, would be sorted right? ...
written 3 months ago by micro32uvas0
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Comment: C: Is my file created completely
... Here's what I have been working on: But somehow this isnt working well on bam filling #!/bin/bash bwa mem -t 48 -M ref.fa data_1.fastq data_2.fastq >mini-data.sam samtools view -b -S -F 2308 -t 48 data.sam >data_unsorted.bam samtools sort data_unsorted.bam data| samtools index ...
written 3 months ago by micro32uvas0 • updated 3 months ago by WouterDeCoster20k

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