User: shuksi1984
shuksi1984 • 10
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Posts by shuksi1984
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... Thanks, I changed the command accordingly and it worked. My command is :
java -jar /path/to/gatk3.8.jar -T RealignerTargetCreator -R /path/to/Homo_sapiens_assembly38.fasta -known/path/to/Homo_sapiens_assembly38.known_indels.vcf -known /path/to/Mills_and_1000G_gold_standard.indels.hg38.vcf -I HG ...
written 1 day ago by
shuksi1984 • 10
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... How to fix the following error?
> ERROR MESSAGE: Fasta index file
> /data/ngs/references/hg38gatkbundle/Homo_sapiens_assembly38.known_indels.vcf.fai
> for reference
> /data/ngs/references/hg38gatkbundle/Homo_sapiens_assembly38.known_indels.vcf
> does not exist
My command is:
j ...
written 1 day ago by
shuksi1984 • 10
• updated
1 day ago by
Devon Ryan ♦ 78k
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... Following shows the complete error.
sh: 1: /data/ngs/mona/RNAseq/genome/genome_file/STAR: not found
"/data/ngs/mona/RNAseq/genome/genome_file/STAR --genomeDir . --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMism ...
written 5 days ago by
shuksi1984 • 10
• updated
5 days ago by
Devon Ryan ♦ 78k
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... Yes, human.refseq.gff.gtf was generated with rsem-prepare-reference. The same file was used during indexing with STAR. ...
written 6 days ago by
shuksi1984 • 10
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... Hi,
I ran following command:
/path/to/rsem/rsem-calculate-expression -p 2 --output-genome-bam -star --star-path /path/to
/STAR_index_files --paired-end path/to/SRR925687_1.fastq path/to/SRR925687_2.fastq human.refseq.gff.gtf path/to/RNA.test
I got following error msg:
dFilesIn SRR925687 ...
written 6 days ago by
shuksi1984 • 10
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... Thanks, but tried the other way.
1.Downloaded the zipped file in my local machine through web.
2.Copied the zipped file in server through SCP.
3.Unzipped and installed.
It worked...! ...
written 6 days ago by
shuksi1984 • 10
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... Yes I did. My command was:
gatk VariantFiltration -R /path/to/reference -V /path/to/input.vcf --filterExpression 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > 4.0' --filterName "basic_snp_filter" -o /path/to/out.vcf
The error I got was: ...
written 7 days ago by
shuksi1984 • 10
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... I updated my GATK3 to GATK4. I ran the following command in GATK4:
gatk -T VariantFiltration -R /path/to/reference -V /path/to/input.vcf --filterExpression 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > 4.0' --filterName "basic_snp_fil ...
written 7 days ago by
shuksi1984 • 10
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... I downloaded the fastq.gz from https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?exp=SRX317694&cmd=search&m=downloads&s=seq. But its usless, its 6GB zipped file..after extraction it is 17GB fastq file. Now I am splitting into paired ends using: fastq-dump --split-3 SRR925687. It is taki ...
written 7 days ago by
shuksi1984 • 10
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... After downloading and unzipping I got 17G sra_data.fastq file. But I need paired end data, as per the link it is paired end, but after extraction there is only one fastq file. I am confused at this point of time. ...
written 8 days ago by
shuksi1984 • 10
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