User: agata88

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agata88460
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Poland
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Posts by agata88

<prev • 207 results • page 1 of 21 • next >
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Comment: C: How to create scaffolds from contigs?
... Thanks I'll try that, although I would like to do it as much automatic as possible :) extracting manually consensus sequence is not comfortable in this case. ...
written 3 days ago by agata88460
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Comment: C: How to create scaffolds from contigs?
... Thanks but velvet does not support higher kmer length than 31. I see that Spades and IDBA need fastq files as input not contig file. Do you know any tool that can concatenate contings into scaffolds with the use of contig fasta file? ...
written 3 days ago by agata88460
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How to create scaffolds from contigs?
... Hi all! I was using velveth and velvetg to create contigs.fa file. It includes all sequences with kmer=31, min contig length 100 and expected coverage 5. Now I would like to create scaffolds, which tool do you recommend for this purpose? Thanks in advance, Best, Agata ...
de novo written 3 days ago by agata88460
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Answer: C: what I want to do after the PhD?
... I would say that "I would like to join team which is involve in making good science, deep research, high quality." That is my goal for the future, although I ma not PhD yet. Postdoc? I think that will come with time based on the scientific achievements. Best, Agata ...
written 11 days ago by agata88460
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Comment: C: How to use qiime group_significance.py script?
... This looks good ... I think I am going to use that first, thank you :) ...
written 4 weeks ago by agata88460
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Comment: C: How to use qiime group_significance.py script?
... I don't think this will help ... especially when I need to compare eg 35 vs 15 samples. I think I need to use group_significance.py script with specified mapping file. I just don't know if I need to check data for normal distribution. Can I assume that all data is not normally distributed? (because ...
written 4 weeks ago by agata88460
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Comment: C: PDB files: Valence error
... It looks like your structure has extra connections coming from O and C in defined positions which is not correct. Best, Agata ...
written 4 weeks ago by agata88460
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Comment: C: PDB files: Valence error
... I am not specialist in PDB sanitization (not sure what it is), but the first thing that I saw was those valence values..5 for C and 3 for O? I think it should be 2 or 4 for C and 2 for O ... and the error tells you that ... Best, Agata ...
written 4 weeks ago by agata88460
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How to use qiime group_significance.py script?
... Hi all! I know that maybe this is not a question for this forum but I will be glad if somebody could give me an advice in that. I would like to compare bacteria abundances (otu_table.biom, qiime) for two groups of samples: * 35 samples with disease * 15 controls I am not sure which test from gr ...
qiime written 4 weeks ago by agata88460
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Comment: C: Consensus secondary RNA stractures
... Do you has it as sequences? If so, you can perform aligment (ClustalO) and then use one form this post: https://www.biostars.org/p/77762/ Best, Agata ...
written 4 weeks ago by agata88460

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For normalization of NGS results
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