User: Cherry

gravatar for Cherry
Cherry50
Reputation:
50
Status:
New User
Location:
Germany
Last seen:
4 years, 10 months ago
Joined:
6 years, 3 months ago
Email:
z********@gmail.com

Posts by Cherry

<prev • 13 results • page 1 of 2 • next >
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phylogeny using 2 alleles per loci data
... Hello everyone, I want to construct a phylogeny based on fasta sequences. Two sequences which contain two alleles stand for one individual, for example: >indi_1_allele1 AATTCGC  >indi_1_allele2 ACTTAGC >indi_2_allele1 ACGTAGC >indi_2_allele2 ACGTATA  ...   Does anyone know ho ...
phylogeny alignment written 5.4 years ago by Cherry50 • updated 5.4 years ago by h.mon32k
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Answer: A: No filtering occuring with GATK'S VariantFiltration Walker
... Have you tried to use floating number when writing the command? (--filterExpression "MQ < 30.0") ...
written 5.7 years ago by Cherry50
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Comment: C: Is it possible to map the Miseq data to the reference?
... It is quite expensive. Usually, it is used only for de novo, I guess. ...
written 5.9 years ago by Cherry50
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Comment: C: Is it possible to map the Miseq data to the reference?
... Thanks, Jn.Golovina. ...
written 5.9 years ago by Cherry50
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Comment: C: Is it possible to map the Miseq data to the reference?
... Hi, Devon, Thanks for your quick replay! I will try it! ...
written 5.9 years ago by Cherry50
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Is it possible to map the Miseq data to the reference?
... Hi, everyone, I would like to know some info about SNPs in one species but only MiSeq data is available. So my question is: Is it possible to map MiSeq data to a reference using mapping software (e.g. bwa or stampy) and then call SNPs using GATK? Any suggestion would be appreciated! Thanks in advan ...
next-gen alignment snp written 5.9 years ago by Cherry50 • updated 5.9 years ago by Evgeniia Golovina1.0k
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What's the meaning of Tags generated by stampy
... Hello everyone! I am confused with the tags in sam files generated by stampy. I have checked the documents of stampy and it said that: "Stampy computes posteriors and likelihoods both for pairs of reads, and for reads considered by themselves. The following table summarizes the SAM tags for these ...
next-gen sequencing written 6.2 years ago by Cherry50 • updated 6.1 years ago by Biostar ♦♦ 20
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Comment: C: stampy install error??
... Hi airan, thanks a lot! Actually, I have read but I failed to fix it. Anyway, I will try to install python again and then stampy. Hope it will work! ...
written 6.2 years ago by Cherry50
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Comment: C: stampy install error??
... I typed "./stampy.py --help" and I got: Could not import the maptools module -- does the maptools.so library exist? Traceback (most recent call last):   File "./stampy.py", line 14, in <module>     import maptools   File "maptools.pyx", line 4, in init maptools (pyx/maptools.c:25713)   File " ...
written 6.2 years ago by Cherry50
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Comment: C: stampy install error??
... Hi airan, Nothing else. That were all the messages I have got. Did I succeed or fail to install? ...
written 6.2 years ago by Cherry50

Latest awards to Cherry

Popular Question 4.9 years ago, created a question with more than 1,000 views. For Erro while converting .SRA File to .fastq File with SRA Toolkit
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Erro while converting .SRA File to .fastq File with SRA Toolkit
Scholar 5.7 years ago, created an answer that has been accepted. For A: No filtering occuring with GATK'S VariantFiltration Walker

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