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3. picard MarkIlluminaAdapters for Non-Illumina Adapters Error

Thank you for the advise...Appreciated.

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• Adi Abuali
• April 09, 2021 14:56
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3. picard MarkIlluminaAdapters for Non-Illumina Adapters Error

Thank you SkyWarrior...I  know it's not GATK tool as well, but if you advice for MGI fastp tool as well for same approach ?

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• Adi Abuali
• April 07, 2021 21:13
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1. Tool Index
2. 4.2.0.0
3. ReadsPipelineSpark (BETA)

What BWA MEM parameters used in this pipleline (e.g. -M, -a,..etc.)? -M mark shorter split hits as secondary -a output all alignments for SE or unpaired PE    

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• Adi Abuali
• April 03, 2021 11:46
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3. MGI DNBSEQ-T7 DNA Sequencer (Nebula) ….Is it Compatible with GATK Best Practice Pipeline?

Thank you SkyWarrior...

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• Adi Abuali
• April 02, 2021 23:08
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1. Tool Index
2. 4.2.0.0
3. ReadsPipelineSpark (BETA)

In case of unaligned BAM (with --align parameter), Will this ReadsPipelineSpark follow the below process (Namely the MergeBamAlignment to include the  tags, RG, UQ, MC, and MQ): https://gatk.broadi...

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• Adi Abuali
• April 02, 2021 23:06
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3. picard MarkIlluminaAdapters for Non-Illumina Adapters Error

Finally it works with below syntax: gatk MarkIlluminaAdapters I=/mnt/d/gen/uAdi.bam O=/mnt/d/gen/uAdi.bam_mark.bam M=/mnt/d/gen/metrics.txt ADAPTERS=null FIVE_PRIME_ADAPTER=AAGTCGGATCGTAGCCATGTCGTT...

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• Adi Abuali
• March 23, 2021 21:17
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3. picard MarkIlluminaAdapters for Non-Illumina Adapters Error

Hi Genevieve, Thanks but I tried this before and it gave me different error as below: picard MarkIlluminaAdapters -I /mnt/d/gen/uAdi.bam -O /mnt/d/gen/uAdi.bam_mark.bam -M /mnt/d/gen/metrics.txt --...

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• Adi Abuali
• March 23, 2021 20:44
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