User: Jautis

gravatar for Jautis
Jautis260
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260
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6 months, 1 week ago
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3 years, 5 months ago
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Posts by Jautis

<prev • 82 results • page 1 of 9 • next >
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Comment: C: Convert an altered sam file into a bam file
... Thanks! I went ahead and added the first 25 lines to the initial question. Yes, I am keeping the same header that I initially generated. I am adding additional fields (NM, MD, XM, XR, and XG flags with dummy values) ...
written 7 months ago by Jautis260
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Convert an altered sam file into a bam file
... Hi, I have a sam file from BSMap which I have modified into the format of a sam file from bismark. However, after doing so, I'm no longer able to convert the sam file into a bam file using samtools. What is it that I'm missing? The more general version of this question would be when are you able t ...
bam sam sequencing written 7 months ago by Jautis260
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BSMap to Bismark bam file formats
... Hi, I'm wondering how to go about transforming a file between different bam formats. In particular, I am interested in switching a file mapped with BSMap into the Bismark bam file format for downstream analyses. I want to do so because BSMap, from simulations I've run, maps heterospecific reads with ...
sequencing next-gen bisulfite bam written 7 months ago by Jautis260
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Comment: C: Genotype calls for a list of variable sites
... That's useful, but is there a way to always call the sites, even if there isn't enough information to identify a variable site in the new dataset? ...
written 9 months ago by Jautis260
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Genotype calls for a list of variable sites
... Hi, I have a list of variable sites identified in a previous study of the same population. I would like to call genotypes in a set of new samples specifically at those sites. How can I do so? I think this is a mix between -L commands to select a particular chromosome region and using a dbSNP fil ...
variant-calling gatk genotype-calling written 9 months ago by Jautis260 • updated 9 months ago by Pierre Lindenbaum110k
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Comment: C: Modifying fasta file based on vcf information
... I used the GATK method suggested by Ashutosh Pandey. It worked pretty well ...
written 13 months ago by Jautis260
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Comment: C: Outputting DP4 flag in GATK
... So that appears similar to DP4, but I need it in DP4 rather than the set of 8 values StrandAllelesCountsBySample would give. I'm piping the vcf into another program and I'm not familiar enough with how that one runs to modify it to use SAC instead. ...
written 15 months ago by Jautis260
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Outputting DP4 flag in GATK
... Hello, is there any way to output DP4 (as well as DP) while using GATK's Haplotype Caller to call variants? Thanks! ...
variant calling gatk sequencing written 15 months ago by Jautis260 • updated 15 months ago by Santosh Anand3.5k
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Comment: C: Getting reads that end at a digest site from a sam/bam file
... I don't think samtools does what I want it to here. I want reads that *end* at an Msp1 digest site, not those that include a digest site anywhere within the read. Using biopython works perfectly for the first part, thank you! ...
written 16 months ago by Jautis260
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Comment: C: Getting reads that end at a digest site from a sam/bam file
... Hi Pierre, because the library was digested I don't expect the reads to actually end with the full Msp1 cut site and would like to retain a read that only had the C or CCG. Additionally, the library is bisulfite converted, so just looking for CCGG at the ends of a read won't work. Rather, I believe ...
written 16 months ago by Jautis260

Latest awards to Jautis

Popular Question 8 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 9 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 12 months ago, created a question with more than 1,000 views. For Calling SNPs from RRBS data
Popular Question 14 months ago, created a question with more than 1,000 views. For Comparing two phylogenies
Popular Question 20 months ago, created a question with more than 1,000 views. For Modifying fasta file based on vcf information
Student 2.8 years ago, asked a question with at least 3 up-votes. For Comparing two phylogenies
Scholar 3.0 years ago, created an answer that has been accepted. For A: SNPs, genotypes, HWE in GWAS,
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Calculating the bisulfite conversion rate
Scholar 3.2 years ago, created an answer that has been accepted. For A: SNPs, genotypes, HWE in GWAS,

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