User: szuszmok

gravatar for szuszmok
szuszmok40
Reputation:
40
Status:
New User
Location:
Hungary
Last seen:
2 years, 5 months ago
Joined:
3 years, 6 months ago
Email:
a**************@gmail.com

Posts by szuszmok

<prev • 24 results • page 1 of 3 • next >
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Sensitivity of variant calling
... Hi All, can someone recommend for me a tool besides GATK - GenotypeConcordance module, which can calculate the variant calling sensitivity from the comparison of two .vcf files? Many thanks!   ...
variant-calling next-gen sequencing written 2.4 years ago by szuszmok40 • updated 2.4 years ago by Len Trigg960
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GATK HaplotypeCaller with strange genotype conc. results
... Hi All, I performed a variant caller comparison, and the genotype concordance analysis of HaplotypeCaller's results a little strange to me, and I can't understand it at all. ALLELES_MATCH:  0  EVAL_SUPERSET_TRUTH:  2438   EVAL_SUBSET_TRUTH: 0   ALLELES_DO_NOT_MATCH: 636   EVAL_ONLY: 20    TRUTH_ON ...
variant calling snp written 2.5 years ago by szuszmok40
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5 follow
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Venn diagram with 11 sets
... Hi All, can anyone recommend me a tool/package, which allows me to create Venn diagrams up to 11 sets? The packages which I have found so far can support to create less sets only. Many thanks! ...
R venn diagram statistics written 2.5 years ago by szuszmok40 • updated 2.5 years ago by Mary11k
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Comment: C: Bowtie2 run out of memory
... The 'funny' thing is that bowtie2 executed almost like a sec. I think that perhaps my fastq data isn't correct. Thanks for your consideration! ...
written 2.5 years ago by szuszmok40
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Comment: C: Bowtie2 run out of memory
... I'm using the 2.2.5 version ...
written 2.5 years ago by szuszmok40
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Comment: C: Bowtie2 run out of memory
... but before this run, I used this configuration with succes, even when Bowtie2 run for human sequence alignment ...
written 2.5 years ago by szuszmok40
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Bowtie2 run out of memory
... Hi All, I tried to run bowtie2 with some simulated paired-end sequences, and I got a strange error. I'm using a virtual machine, I got for this VM environment 8 Gb RAM, so I assumed that this could be enough even in case of human data... Besides, before this run I used bowtie2 successfully. Anyone ...
software error bowtie2 alignment written 2.5 years ago by szuszmok40
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Comment: C: cannot read data from simulated FASTQ files
... I'm sure that the path is correct. ...
written 2.5 years ago by szuszmok40
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cannot read data from simulated FASTQ files
... Hi All, after some suffering I realized, that perhaps my simulated paired-end fastq files are not correct in some way. (I found in Bowtie2 log 'no input read files were valid' and Trimmomatic couldn't handle these files either) So, below there is a part of one of my paired end sequences, I don't k ...
fastq fileformat written 2.5 years ago by szuszmok40 • updated 2.5 years ago by Antonio R. Franco3.4k
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Comment: C: Trimmomatic error java.io.FileNotFoundException
... yes, but it is normal, that Trimmomatic using '0 forward/reverse sequences' even if I have paired-end sequences? or that using 0 sequences at all? ...
written 2.5 years ago by szuszmok40

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