User: kspata

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kspata60
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Posts by kspata

<prev • 86 results • page 1 of 9 • next >
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Comment: C: differences between Illumina Platinum Variant Calls and NIST variant calls
... I have edited my post. Thank you !! ...
written 4 weeks ago by kspata60
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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 4 weeks ago by kspata60
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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 10 weeks ago by kspata60
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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 10 weeks ago by kspata60 • updated 10 weeks ago by WouterDeCoster40k
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Variant discrepancy between technical replicates
... I am performing alignment to reference and variant calling for same sample using freebayes. Both the technical replicates were sequenced on MiSeq PE 250. The raw data was trimmed using trim galore with `Q > 30 and length >= 200`. The trimmed reads were mapped using bowtie2 to the reference seq ...
alignment freebayes written 3 months ago by kspata60 • updated 3 months ago by geek_y9.8k
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Error running samjdk.jar for extracting reads containing indels
... Hi All, I want to extract all reads containing a variant from a co-ordinate sorted bam file. The variant is an 11 bp long insertion starting at base position 39. I am running `samjdk.jar` script as per instructions in the post here: https://www.biostars.org/p/283969/ I modified the input file Scr ...
samjdk jvarkit alignment indels written 4 months ago by kspata60
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Comment: C: Effect of trimming on alignment and fastqc report.
... Thank you for explanation. I have learned a lot through this post !!! ...
written 4 months ago by kspata60
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Comment: C: Effect of trimming on alignment and fastqc report.
... Thank you!! Changing the parameter to `--very-sensitive-local` did not alter the variant call result. I also tried `end_to_end` but that also gave the variant at same frequency. I appreciate the help. I am beginning to understand how the alignment algorithms work more. ...
written 4 months ago by kspata60
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Comment: C: Effect of trimming on alignment and fastqc report.
... I first performed trimming with trim galore trim_galore -q 30 --length 200 -a AGATCGGAAGAGC --no_report_file --paired Sample.R1.fastq.gz Sample.R2.fastq.gz 2> Sample.trim_galore.err Then I trimmed these reads using the following command for trimmed.R1.fq and trimmed.R2.fq awk '{un ...
written 4 months ago by kspata60
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Comment: C: Effect of trimming on alignment and fastqc report.
... Hi Genomax, I checked again to confirm only reads with bases having Quality greater than 30 were selected. So I am confused about the fastqc results as well. I understand trimming is severe but less stringent trimming is leading to a false variant call at much higher frequency. Can you please ref ...
written 4 months ago by kspata60

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Popular Question 4 months ago, created a question with more than 1,000 views. For Convert blastn to gff3
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