User: anjali.gopal91

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New User
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United States
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4 years, 9 months ago
Joined:
6 years, 5 months ago
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Posts by anjali.gopal91

<prev • 14 results • page 2 of 2 • next >
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Answer: A: Multisample SNP/SNV calling - What's your favourite method?
... I haven't really worked with pooled data (if that's what you mean by multi-sample SNP calling) but I've been using SNVer, and it works great. One thing I really like about it is that it lets you define the ploidy of your sample, which is helpful for me since I work with haploid yeast data a lot. Sam ...
written 6.1 years ago by anjali.gopal9150 • updated 15 months ago by _r_am32k
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Getting pileup information from Sam files
... I'm working on a project where I'm aligning fastq files that contain sequence information about a series of small ORfs (usually ~2 kb in size). These were all contained in bacterial entry vectors (i.e., plasmids). I'm using bowtie2 to align these sequences, but would like to determine the pileups s ...
gene alignment next-gen sequencing written 6.4 years ago by anjali.gopal9150 • updated 6.4 years ago by Devon Ryan98k
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Answer: A: SNVer error: chrome not found in Reference
... Never mind, I fixed this. Turns out my bam file was not sorted. If anyone else has this error, you can get around it by: samtools sort [filename].bam [output] ...
written 6.4 years ago by anjali.gopal9150
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SNVer error: chrome not found in Reference
... Hi all, I'm pretty new to bioinformatics, so please bear with me if I'm using incorrect terminology. I'm trying to perform variant calling on a series of genes (NOT a whole genome). I have a fasta file that has reference sequences for all of these genes, and a series of fastq files for reads. I al ...
software error variant calling written 6.4 years ago by anjali.gopal9150 • updated 4.5 years ago by rse90

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