User: kspata

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kspata40
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1 year, 9 months ago
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Posts by kspata

<prev • 44 results • page 1 of 5 • next >
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Current version of human reference Genome Assembly
... Hi, I wish to perform variant analysis for exon capture data. The samples are human tissue samples. I already have the sequencing data and the list of exons to analyze. The exon co-ordinates are taken from the GCF_000001405.38 assembly. I looked up on the UCSC genome browser and there the hg38 ass ...
genome assembly reference written 20 days ago by kspata40 • updated 20 days ago by vkkodali450
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reformat forward and reverse read pairs for variant analysis of exons
... Hi, I have exon capture data for 10 genes. The exon capture and amplification was done by Agilent SureSelect XT capture kit. The amplicons were sequenced on NextSeq 2X150 bp. I wish to analyze the exonic variants for the 10 genes. The protocol which I have is: 1) Trim data to remove adapters and lo ...
variant calling assembly exon capture gene written 21 days ago by kspata40
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Comment: C: de novo assembly of circular plasmid
... Hi Piet, Thank you for responding. I performed a resequencing analysis, in which I mapped the reads to the reference using BWA and performed variant calling apart from 1 insertion of CG at position 6354 and 2 insertions at positions 10384 of 22 bp long and 10349 of 4 bp long, there are no more varia ...
written 7 weeks ago by kspata40
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de novo assembly of circular plasmid
... Hi All, I have a circular plasmid sample which was sequenced on MiSeq PE 300. I performed a de novo aseembly using `SPAdes.` The contig which I obtained is 11526 bp long. The reference sequence for this plasmid is 12089bp long. When I BLAST the reference sequence against the de novo assembled conti ...
de novo assembly spades plasmids written 7 weeks ago by kspata40 • updated 7 weeks ago by piet1.6k
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Strategy to detect deletions in the PE 300 reads
... Hi All, I have PE 300 sequencing data of a circular plasmid sample. I want to detect deletions which occur at low frequency with deletion length in the range of 20bp to 50 bp. What tools can I use to detect these variants. Samtools was not able to detect these deletion variants. Thanks!!! ...
assembly sequencing snp indels written 8 weeks ago by kspata40
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Comment: C: Deletions in a consensus sequence.
... Hi Fin, I have performed variant calling but these variants are not called with samtools as they are very large deletions (>35bp) present at low frequency (<10%). Even if they are at low frequency I wish to include them in the consensus sequence. So that when I perform BLAST of reference vs c ...
written 8 weeks ago by kspata40
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Deletions in a consensus sequence.
... Hi All, I performed alignment of merged forward and reverse read for a plasmid sequence. From this I wanted to observe deletion in a specific location. I extracted all reads from the BAM file in the region 10000-10040. I found that around 600 reads mapped to this position and out of them 200 had de ...
deletions alignment consnesus sequence sequencing written 8 weeks ago by kspata40
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Deletion detected at less frequency than expected for a plasmid sample
... Hi, I was performing variant analysis for a plasmid sample sequenced on MiSeq with read length PE300. More than one million reads were generated. The mapping rate of the reads to the reference was 98%. I used samtools to detect variants and generate consensus sequence. 3 variants were detected for ...
assembly alignment written 9 weeks ago by kspata40 • updated 9 weeks ago by RamRS19k
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Comment: C: download genbank sequences with exon sequences highlighted
... Hi genomax, Thank you for replying. Your suggestion is the most close to what I need. Also, on Ensemble you can download the sequence with exons highlighted in the RTF (Rich Text Format). [https://useast.ensembl.org/Homo_sapiens/Gene/Sequence?g=ENSG00000133703;r=12:25204789-25250936][1] However, ...
written 3 months ago by kspata40
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download genbank sequences with exon sequences highlighted
... Hi, I wish to download genbank sequence for KRAS with all the exonic regions highlighted. GenBank has an option of 'Highlight Sequence Feature' which displays exons one at a time. But I want to highlight these sequences (exons only) in the downloaded GenBank file. [https://www.ncbi.nlm.nih.gov/nuc ...
gene genbank written 3 months ago by kspata40 • updated 3 months ago by Dattatray Mongad200

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