User: kspata

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kspata70
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Chicago
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1 week, 3 days ago
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3 years, 8 months ago
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Posts by kspata

<prev • 100 results • page 1 of 10 • next >
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Comment: C: Extract unique barcodes and find their frequency
... Thanks for replying. I know the location of the barcodes in the reference which is from base pair 807-896. I do not know their sequence or location in the reads. Will bbduk work in this way? ...
written 11 days ago by kspata70
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Extract unique barcodes and find their frequency
... Hi All, I have paired end 250 sequencing data for a sample. The read count is around 2 million. The data has 70-mer barcodes which are embedded in common upstream and downstream region. I have to analyze how many unique barcodes are present in the sample and their frequency relative to total numb ...
illumina ngs mapping written 11 days ago by kspata70
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Comment: C: Read showing Insertion of 41 bases when aligned with BWA
... The total depth at this location is 1300 (Reference Reads + Alternate Reads). The variant is found at 10% frequency. This reads map to the ITR regions. Some bases are automatically softclipped by the aligners. Also, the variants are located in the reverse reads. ...
written 3 months ago by kspata70
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Comment: C: Read showing Insertion of 41 bases when aligned with BWA
... Hi swbarnes2, I dont understand what you mean to say. I understand BWA is introducing inserts instead of soft clipping. I dont know why this is happening. Also, this region is ITR and contains CCCGGG repeats. Does BWA forcefully introduce inserts to obtain high alignment score? ...
written 3 months ago by kspata70
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Read showing Insertion of 41 bases when aligned with BWA
... Hi All, I aligned reads of a viral vector using both Bowtie2 local and BWA-MEM. 1300 reads are mapped to this position. I observed that BWA shows an insert of 41 bases (in the ITR region), the mapping quality of this read is 60, AS:i:91 and CIGAR string of 53S91M41I7M27I4M. While bowtie2 local d ...
bowtie2 variant bwa written 3 months ago by kspata70 • updated 3 months ago by swbarnes28.9k
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Annotation of non model fish (mahi mahi) genome
... Hi, I have an assembled genome obtained from oxford nanopore reads. How can I perform a basic annotation to obtain a genbank file? What tools are available to perform eukaryotic genome annotation. I had previously used RAST for bacterial genome annotations, can I use this tool for eukaryotic gen ...
assembly annotation written 3 months ago by kspata70 • updated 3 months ago by Shalu Jhanwar470
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Detect Transgene Insertion Site using SAM format
... Hi All, I am working on identifying insertion site and copy number of a retroviral vector integration in human cell line. The sample was sequenced by WGS on NextSeq with around 900 million PE150 reads. I concatenated hg38 and the vector genome and mapped reads to this combined reference using BWA. ...
transgene insertion site sam tools bwa written 7 months ago by kspata70
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Comparative analysis of experimental and control data from BS seq run
... Hi All, I have one control sample and 3 experimental samples sequenced on HiSeq using Bisulfite sequencing protocol. I aligned the reads to the hg38 genome and performed methylation calls using standard Whole Genome Bisulfite bismark pipeline. I wish to perform comparative analysis between experim ...
bs seq cpg annoattion bismark written 9 months ago by kspata70
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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 10 months 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 13 months ago by kspata70

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