User: arjun.murthy779

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Posts by arjun.murthy779

<prev • 10 results • page 1 of 1 • next >
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Fasta Indexing for SNP Analysis
... Hi! I am trying to carry out an SNP Analysis on Mycobacterium tuberculosis sequences. I am unfortunately not able to annotate it, and think the problem lies with the fasta index and dictionary files, which were created The accession number of the fasta sequence is >NC_018143.2. When I run a fas ...
snp bacterium written 7 months ago by arjun.murthy77910
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SNP Annotation on Mycobacterium tuberculosis vcf files
... Hi! I've been trying to annotate Mycobacterium tuberculosis files, as a part of the SNP pipeline. I currently have the Mtb .vcf files in hand, and am not able to use SNPEff tool to carry it out. Any advice on how to proceed further would be greatly appreciated! Thank you! ...
snp bacterium written 7 months ago by arjun.murthy77910
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SNP Feature File Indexing
... Hi! I am trying to index a SNP vcf file so that I can run a base recalibration on it. I have generated a first round filtered variant file, which I am indexing and using to run the Base recalibration. The code I am using for this is: gatk IndexFeatureFile -F ref_1_filteredSNP.vcf It is throwing me ...
genome snp bacterial written 7 months ago by arjun.murthy77910
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Comment: C: BQSR Recalibration for Mycobacterium Genome Data
... Thank you! This seems like it should work ...
written 7 months ago by arjun.murthy77910
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BQSR Recalibration for Mycobacterium Genome Data
... Hi, We are trying to run an SNP Analysis on Mtb whole genome. Currently, we are stuck at the Base Recalibration Step. It says that we require a DbSNP file to generate the BQSR.table for Applying BQSR. The DbSNP file for Mycobacterium tuberculosis does not exist. Any advice on how to move forward wi ...
bqsr snp written 7 months ago by arjun.murthy77910 • updated 7 months ago by 54354165620
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Comment: C: Problems in Variant Calling Code
... Hi Kevin. Thank you for the clarification, This makes more sense to me now. I had picked up the code as I am quite new to this field. I have another question regarding SNP Analysis. How would you carry out the Base Recalibration and Apply BQSR step for a Bacterial genome. I am sharing the code I ...
written 7 months ago by arjun.murthy77910 • updated 7 months ago by _r_am30k
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SNP Feature File
... I am a bit confused on how to generate a SNP Feature File for Mycobacterium tuberculosis. I am trying to carry out a SNP Analysis on the different strains in Mycobacterium tuberculosis. My understanding is that we need to generate a SNP Feature File which is to be used for the Base Recalibration st ...
snp bacterium written 7 months ago by arjun.murthy77910
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Problems in Variant Calling Code
... I am not able to understand this code snippet I have, to carry out variant calling, for the SNP Analysis. The snippet is: **bcftools mpileup -Ou -f Ref_1_20040804.fa ref_1.sorted.bam | bcftools call -mv -Ob -o ref_1_btool.bcf** **bcftools view ref_1_btool.bcf > pile.vcf** **bcftools call -cv ...
variant calling snp written 7 months ago by arjun.murthy77910
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Comment: C: Alignment of two .fa Files
... Alright, let me try to put it in better words. I have downloaded a bunch of reference genomes of a specific bacterium (say 100), which is spread over 10 years. I have the oldest submitted sequence (say 2003). Now, I am trying to align the 2003 sequence with another reference sequence (say submitted ...
written 10 months ago by arjun.murthy77910
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Alignment of two .fa Files
... For SNP Analysis, you need to create an alignment of two files. Generally you use a .fa and .fq files. How would you carry out alignment using two .fa files (Reference genomes from NCBI)? Bowtie2 and Bwa tools are not carrying out the alignment correctly. ...
alignment written 10 months ago by arjun.murthy77910 • updated 10 months ago by Mensur Dlakic7.1k

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