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User: a.alnawfal.1992

gravatar for a.alnawfal.1992
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Posts by a.alnawfal.1992

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Need help with STAR aligner
... Hi Zeinab, if your laptop's RAM lower than 32 GB , it will not work, actually you can start alignment but after same time the process going to stop and you will get a massage like 'Process Killed'. I have used STAR for Human data analysis and it's very powerful tool and super fast. As our colleges ...
written 4 weeks ago by a.alnawfal.1992 • 40
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Answer: A: quality check of vcf files
... Hi, there are a lots of tools give you sammuray about you VCF file, like: vt vt peek GATK gatk VariantEval rtg-tools rtg vcfstats BCF-Tools bcftools stats and a lot more tools do the same, as i do not know what is you experiments and you goal (what you want to do exact ...
written 4 weeks ago by a.alnawfal.1992 • 40
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Comment: C: How to calculate mutation rate and mutation sites in a genome using FASTA file?
... you answer make me confused !! are trying to convert to Fasta or Fastq ?! assuming that you are trying to convert **Fasta to Fastq** without Quality score file: first of all, Fasta contains only the sequence information and lacks of quality information, unlike Fastq where both are there in fourth an ...
written 5 weeks ago by a.alnawfal.1992 • 40
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Answer: A: How to calculate mutation rate and mutation sites in a genome using FASTA file?
... according to what i understood, you have read from 6 viral genome in "**Fasta**" format and you want to aligned them in order to identified mutations ? do you have **Qual** file? if yes do the below conversion with **biopython** from Bio import SeqIO from Bio.SeqIO.QualityIO import PairedF ...
written 5 weeks ago by a.alnawfal.1992 • 40
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Comment: A: bwa mem | samtools sort failing without any error messages
... First you need to **decompress** your .fastq files and **index** the reference , try the below command : bwa mem -t 24 GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna R1.fq R2.fq | samtools view -bS - > FinalBAM.bam The '-' in samtools view tells it to read from stdin i hope i ...
written 5 months ago by a.alnawfal.1992 • 40

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Scholar 4 weeks ago, created an answer that has been accepted. For A: Need help with STAR aligner
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