User: shuksi1984

gravatar for shuksi1984
shuksi198410
Reputation:
10
Status:
New User
Location:
Last seen:
2 hours ago
Joined:
2 weeks, 1 day ago
Email:
s*********@gmail.com

Posts by shuksi1984

<prev • 21 results • page 1 of 3 • next >
0
votes
1
answer
70
views
1
answers
Comment: C: GATK3 error while performing local realignment for exome
... 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 shuksi198410
1
vote
1
answer
70
views
1
answer
GATK3 error while performing local realignment for exome
... 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 ...
software error next-gen sequencing written 1 day ago by shuksi198410 • updated 1 day ago by Devon Ryan78k
0
votes
0
answers
63
views
0
answers
Comment: C: RNAseq error while running sem-calculate-expression
... 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 shuksi198410 • updated 5 days ago by Devon Ryan78k
0
votes
0
answers
63
views
0
answers
Comment: C: RNAseq error while running sem-calculate-expression
... 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 shuksi198410
0
votes
0
answers
63
views
0
answers
RNAseq error while running sem-calculate-expression
... 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 ...
software error rna-seq sequencing written 6 days ago by shuksi198410
0
votes
1
answer
71
views
1
answers
Comment: C: GATK current version downloading fails
... 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 shuksi198410
0
votes
1
answer
75
views
1
answers
Comment: C: GATK error while performing WES for the HG100 downloaded from 1000genomes
... 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 shuksi198410
0
votes
1
answer
75
views
1
answers
Comment: C: GATK error while performing WES for the HG100 downloaded from 1000genomes
... 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 shuksi198410
0
votes
1
answer
119
views
1
answers
Comment: C: RNAseq raw data for expression analysis
... 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 shuksi198410
0
votes
1
answer
119
views
1
answers
Comment: C: RNAseq raw data for expression analysis
... 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 shuksi198410

Latest awards to shuksi1984

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1734 users visited in the last hour