User: kspata

gravatar for kspata
kspata70
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70
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Location:
Chicago
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6 days, 19 hours ago
Joined:
2 years, 11 months ago
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k*****@gmail.com

Posts by kspata

<prev • 92 results • page 1 of 10 • next >
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Calculate LOH score for tumor only sample using GenomeStudio
... Greetings, I wish to calculate LOH sores of around 80 tumor only samples using GenomeStudio. In the Analysis tab of genome studio I can see paired sample analysis, but my samples are tumor only samples and don't have corresponding reference samples. How can I calculate LOH scores for tumor only sa ...
loh score infinium assay genomestudio genotyping written 5 weeks ago by kspata70
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Comment: C: sh: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8)
... It does not return a blank line. It returns an ip address. 192.168.2.130 51954 22 ...
written 4 months ago by kspata70
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Comment: C: sh: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8)
... I believe am connected via ssh. Although I am not sure how to check it. The `top` command output 18149 callie_ 20 0 104m 4108 1084 S 8.3 0.0 4:53.61 sshd The `who i am` output callie pts/0 Sep 16 14:13 (mb02-002.com) ...
written 4 months ago by kspata70
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Comment: C: sh: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8)
... Hi Joe, There are no commas in the etc environment file. I am still getting the same error, even with the above command export LC_ALL="en_US.utf8" fastqc PhiX_S1_R1_001_val_1.sickle.fq.gz -t 16 perl: warning: Setting locale failed. perl: warning: Please check that your locale s ...
written 4 months ago by kspata70
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Comment: C: sh: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8)
... locale Output: locale: Cannot set LC_ALL to default locale: No such file or directory LANG=en_US.utf8 LC_CTYPE="en_US.utf8" LC_NUMERIC="en_US.utf8" LC_TIME="en_US.utf8" LC_COLLATE="en_US.utf8" LC_MONETARY="en_US.utf8" LC_MESSAGES="en_US.utf8" LC_PAPER="en_US ...
written 4 months ago by kspata70
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sh: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8)
... Hi All, I am running a perl script which integrates several tools like fastqc, bwa, and samtools to call variants. Recently, while calling this perl script I am getting error message as follows: perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: ...
perl bwa bash written 4 months ago by kspata70 • updated 4 months ago by Joe15k
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Comment: C: differences between Illumina Platinum Variant Calls and NIST variant calls
... I have edited my post. Thank you !! ...
written 6 months ago by kspata70
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differences between Illumina Platinum Variant Calls and NIST variant calls
... Hi All, I am validating a bioinformatics pipeline for SNP and INDEL calling. For this purpose I mapped the reads from Illumina Platinum Genome ([https://www.ebi.ac.uk/ena/data/view/ERR194147][1]) to hg38 assembly ([ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome ...
vcf snp written 6 months ago by kspata70
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Comment: C: Validation of SNP and INDEL calling pipeline
... @wouterDeCoster, Thank you for your input. But we don't have the system capacity to analyze whole genome data and map it to the entire human genome reference. I used data in the above link and mapped to chr21 which gives very less average per base coverage of 3, which is not desired for downstream ...
written 7 months ago by kspata70
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Validation of SNP and INDEL calling pipeline
... Hi, I am validating an in-house pipeline for calling SNP and INDELS for small genomes. For this purpose I am using the GIAB NA12878 HiSeq 2500 300X coverage dataset. ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/131219_D00360_005_BH814YADXX/Project_RM8398/Sam ...
genome indel alignment snp written 7 months ago by kspata70 • updated 7 months ago by WouterDeCoster42k

Latest awards to kspata

Popular Question 9 months ago, created a question with more than 1,000 views. For Convert blastn to gff3
Popular Question 11 months ago, created a question with more than 1,000 views. For Convert blastn to gff3

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