User: ppurkayastha2010

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Posts by ppurkayastha2010

<prev • 6 results • page 1 of 1 • next >
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De-novo assembly of a bacterial genome
... I am trying to assemble a bacterial genome of length 8Mb in **orione.crs4.it** . I could successfully load the paired-end illumina dataset into the server, but I am unable to do the de-novo assembly for the paired end data using any of the programs. Could anyone suggest if the tools are working in ...
orione.crs4.it bacterial genome denovo assembly written 6 months ago by ppurkayastha201010 • updated 6 months ago by Jennifer Hillman Jackson23k
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Aligning more than 2 sequences
... I have a pair-end data fast1.fq and fast2.fq in (fastq format). Now, I need to align the pair-end reads with two reference sequences. I need to align the 3 sequences (pair end file, reference1, and reference 2) in such a way that in a bam file, I can see these three aligned and mapped to each othe ...
variant analysis alignment ngs written 7 months ago by ppurkayastha201010 • updated 7 months ago by Jennifer Hillman Jackson23k
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How to filter SNP and Indel data
... I have mapped my sequence with a wild type sequence using Bowtie2 and obtained around 8000 SNPs and 700 Indels using Varscan. Please let me know how do I further shortlist the SNPs and Indels (based on which criteria)? The output file looks like this POS #CHROM ID REF ALT QUAL FILTER INFO FORM ...
variant analysis snp indels written 8 months ago by ppurkayastha201010 • updated 8 months ago by Guy Reeves1.0k
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How to check unaligned reads?
... I have a pair end SRA files for which I have done FASTQc. The SRA files are then mapped against the reference sequence using Bowtie2. While mapping the paired ends with the reference sequence using Bowtie2 tool of galaxy, I have set an option of writing unaligned reads and aligned reads in separat ...
variant analysis bowtie2 mapping written 8 months ago by ppurkayastha201010
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Comment: C: Bacterial Sequence for Variant Analysis
... How can the steps for human mitochondrial genome used for bacterial genome? ...
written 8 months ago by ppurkayastha201010
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Bacterial Sequence for Variant Analysis
... I am analyzing paired-end data for bacterial genome and have done the following steps: *FASTQC analysis *Trim Galore *Bowtie2 I have got a BAM file after the alignment with reference sequence using Bowtie2. Please let me know what are steps I should follow for variant analys ...
snp rna-seq written 8 months ago by ppurkayastha201010 • updated 8 months ago by m.bernt20

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