User: lleipnitz

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lleipnitz0
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Posts by lleipnitz

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Comment: C: Problems launching Lositan
... Hello h.mon, and thank you for your reply! Sadly, I had read the topics you have posted before, and none of them really helped me solve the problem. At least I learned that, apparently, Lositan is not compatible with recent versions of Java because of its security protocols (version 1.6 is recommend ...
written 8 weeks ago by lleipnitz0
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VCF file conversion to BayeScan format is not working
... Hello all! I am currently having trouble to convert a .vcf file to a bayescan input that takes into account the population information. I have a dataset of 34 individuals divided into 10 populations and over 34K SNPs to analyze. I have tried converting a .vcf file (generated through the STACKS prog ...
vcf next-gen bayescan snp population information written 8 weeks ago by lleipnitz0 • updated 7 weeks ago by Biostar ♦♦ 20
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Problems launching Lositan
... Hello all! I am currently working on an NGS dataset (~34K snps, 34 individuals, 10 populations, RADseq data) and I need to evaluate how many loci are possibly under selection. To do so I intend to use Lositan and BayeScan. While BayeScan runs with no major problems, Lositan does not even open. I a ...
next-gen outliers snp lositan written 8 weeks ago by lleipnitz0 • updated 8 weeks ago by h.mon22k
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Comment: C: Issues building indexed .bam files with SAMtools
... Hello mks002! I tried your command and it worked! Thank you very much! ...
written 6 months ago by lleipnitz0
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Comment: C: Issues building indexed .bam files with SAMtools
... I used "-l 0" because I thought I had to specify that the output should be uncompressed. And no, I am not sure I want to sort by name. Actually now I think I don't have to sort by name because, as h.mon said, to index the files they'd have to be sorted by position, not by name. Thank you very much ...
written 6 months ago by lleipnitz0
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Comment: C: Issues building indexed .bam files with SAMtools
... I thought I should sort by name because then the reads would be in the same order in both the reference and sample aligned to it. So I probably have mistaken sorting by name for sorting by position. If I index both the reference and the .bam file, can they be used in samtools mpileup? As for the r ...
written 6 months ago by lleipnitz0 • updated 6 months ago by h.mon22k
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Issues building indexed .bam files with SAMtools
... Hello all! I am fairly new to bioinformatics and I have been struggling to treat some NGS files I have just received. Here is the thing: I have 35 samples sequenced using the RAD-seq methodology and I have been trying to replicate the pipeline that the company which sequenced my samples used to trea ...
genome assembly alignment rad-seq snp written 6 months ago by lleipnitz0 • updated 6 months ago by h.mon22k

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