User: chase.lewis

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chase.lewis40
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Posts by chase.lewis

<prev • 10 results • page 1 of 1 • next >
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Comment: C: SnpEff: How to match variants with line ID in 1001 Genomes Project?
... I figured it out. I got base pair numbers of interesting mutations from the main file and used grep to find each number in the individual vcf files (non-snpeff files), which I downloaded from the site. Grep reads back the file name if it finds the string in it, if you grep through multiple files as ...
written 14 days ago by chase.lewis40
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SnpEff: How to match variants with line ID in 1001 Genomes Project?
... Hi, I'm trying to use data from the 1001 Genomes Project to solve a problem. There are over a 1000 lines that have already been sequenced, mapped, and analyzed with SnpEff. I want to use this data to see all the variants in a certain gene. I found the file 1001genomes_snp-short-indel_only_ACGTN_v ...
snpeff snp sequencing written 14 days ago by chase.lewis40 • updated 14 days ago by zx87547.5k
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Comment: C: Finding Plasmid Contruct Insertion in Genome through Split Alignment
... That looks like a good tool. ...
written 24 months ago by chase.lewis40
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Answer: A: Finding Plasmid Contruct Insertion in Genome through Split Alignment
... Well, I manged to solve the issue. I aligned the reads to the (Genome+Plasmid) reference using bwa mem without -M function. Then I converted to bam with samtools. I then used the program lumpy (lumpyexpress function) which had a specific built in script that allowed me to extract the split reads an ...
written 24 months ago by chase.lewis40
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Comment: C: Finding Plasmid Contruct Insertion in Genome through Split Alignment
... https://www.biostars.org/p/84641/ In this thread, the answers basically say that bwa mem can make a sam file for me that contains any read where one end maps to one place in the genome and one end maps to another place in the genome. I'm not sure how to get bwa mem to do this for me. Somehow, I gues ...
written 24 months ago by chase.lewis40
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Comment: C: Finding Plasmid Contruct Insertion in Genome through Split Alignment
... The problem is that when I go through all the steps for the programs, then try to extract using SAMtools view (and setting different flags), it does not appear to find any split reads. Is there a typical protocol for finding split reads with programs such as bwa mem? Should I be marking short split ...
written 24 months ago by chase.lewis40
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Comment: C: Finding Plasmid Contruct Insertion in Genome through Split Alignment
... I had not seen that forum. I'm not sure its the exact issue as mine because it seems that their insertion sequence is unknown. I forgot to mention that mine is known, which should make my problem simpler. ...
written 24 months ago by chase.lewis40
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Comment: C: Finding Plasmid Contruct Insertion in Genome through Split Alignment
... I've tried something like this, but I will look into it more. ...
written 24 months ago by chase.lewis40
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Comment: C: Finding Plasmid Contruct Insertion in Genome through Split Alignment
... I've looked online but have not been able to find any program that can open .sam files in a readable form. Basically I have not idea how to open them, so I haven't tried any method. For the alignment tools, when I used bwa-mem, I went through all the steps but did not find any split reads in the end ...
written 24 months ago by chase.lewis40
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Finding Plasmid Contruct Insertion in Genome through Split Alignment
... Hi guys, I am relatively new to alignment tools and bioinformatics in general. I have seen several questions on the forums pertaining to my question, but after following through on the answers, I can't seem to get the right result. Basically, I am trying to find where a plasmid tDNA insertion of kno ...
gene alignment written 24 months ago by chase.lewis40

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Popular Question 23 months ago, created a question with more than 1,000 views. For Finding Plasmid Contruct Insertion in Genome through Split Alignment

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