User: joreamayarom

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joreamayarom120
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120
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USA/Cambridge
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Joined:
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Posts by joreamayarom

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Problems when parsing VCF file with Python
... Thanks for your suggestion. I've contacted the people maintaining the program and they told me there's likely a bug involved. I'll update the question when a solution is ready. ...
written 2.3 years ago by joreamayarom120
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Problems when parsing VCF file with Python
... I'm trying to create sliding windows of a vcf file using Egglib [Egglib's slider method for VcfParser class][1]. My code and the error looks like this: import egglib vcf = egglib.io.VcfParser("20000.vcf") for ret in vcf: print ret #Check if the file was loaded. Everything is ...
vcf python written 2.3 years ago by joreamayarom120 • updated 2.3 years ago by Istvan Albert ♦♦ 81k
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Stampy and malformed BAM files?
... I'm mapping reads in a BAM file to a genome using STAMPY. Apparently, some of my reads are severely malformed and STAMPY is issuing the following complain: stampy: Mapping failed on input line 1742232 of file /path/to/reads/my_file.R2.fastq.gz: CCCFFFFFHHHGHHJJJJJGHIJJIIJGJI@HIIJJJAGHJJIHHHFFFD ...
stampy bam mapping written 2.4 years ago by joreamayarom120
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How good are bwa-mem and stampy when dealing with low quality reads?
... Hi all! I have some Illumina 100bp paired fastq that I'm planning to map to a reference genome. There is a long story about how I got these reads; the important point is that I just receive them without any prior information about their quality or preprocessing, so I decided to run fastqc... Most o ...
mapping bwa written 2.5 years ago by joreamayarom120
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Comment: C: Malformed BAM file produced by BWA
... I'm talking about recommendation 1. In GATK webpage (http://gatkforums.broadinstitute.org/gatk/discussion/2799) they recommend the following command with an -M before -R. `bwa mem -M -R ’’ -p reference.fa raw_reads.fq > aligned_reads.sam` ...
written 2.5 years ago by joreamayarom120
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Comment: C: Malformed BAM file produced by BWA
... I'm checking GATK documentation right now. It is mentioned that the -M flag is essential for Picard compatibility. Is that missing from your answer or you have an specific reason to leave it out? ...
written 2.5 years ago by joreamayarom120
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Malformed BAM file produced by BWA
... I'm aligning reads to a genome to later do some variant calling. I have mapped some reads to a genome using bwa and created the corresponding dictionary bwa index -p ref.fa ref.fa bwa mem ref.fa forward.fastq.gz reverse.fastq.gz -t 16 > mapped_file.sam samtools view -bS mapped_file.s ...
gatk picard samtools written 2.5 years ago by joreamayarom120 • updated 2.5 years ago by Pierre Lindenbaum123k
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How to load megacc output into R?
... I'm using megacc (MEGA's version for DEBIAN) to produce pairwise difference matrices. Now, I want to load the matrices into R for further analysis. MEGA's format looks like this #mega !Title: ; !Format DataType=Distance DataFormat=LowerLeft NTaxa=16; !Description No. of Tax ...
R mega written 2.9 years ago by joreamayarom120
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Create a phylogenetic tree with a bar at the end?
... I have a huge tree stored in newick format and a table with attributes for the tips. Using the package ape, I was able to put common colors to tips and branches that share the same attribute, but I would like to depict a more concrete representation, like a bar at the end, to make clear where my clu ...
phylogeny tree written 3.0 years ago by joreamayarom120 • updated 3.0 years ago by WouterDeCoster41k
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Phylogenies: Is PAUP compatible with ETE 3?
... I have just produced a NJ tree using PAUP and a piece of code that looks like this(https://www.biostars.org/p/81114/, my main reason to use PAUP is explained in the same post). PAUP capabilities to plot trees are relatively limited and since it stores the trees in *.tre format by default, is there a ...
phylogenies paup trees written 3.0 years ago by joreamayarom120 • updated 3.0 years ago by Brice Sarver3.1k

Latest awards to joreamayarom

Popular Question 2.3 years ago, created a question with more than 1,000 views. For Malformed BAM file produced by BWA
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How good are bwa-mem and stampy when dealing with low quality reads?
Appreciated 2.9 years ago, created a post with more than 5 votes. For C: Multiline Fasta To Single Line Fasta
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: Multiline Fasta To Single Line Fasta

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