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Recent Replies
Answer: How to trim sequences
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Mensur Dlakic
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Generally speaking, your don't trim individual sequences. Rather, you align them first and then trim the alignment. I will give you links t…
Comment: Metabat2 (binning package) Error: ReferenceFile: <filename>.fasta is not the sam
by
samdegregori
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@mensur apologies on subjecting you to such a trivial troubleshooting error. Hitting myself on the head because I was thinking fa and fna w…
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You may want to get the data directly from GDC Portal/analysis center for the TCGA data: https://portal.gdc.cancer.gov/analysis_page?app=Pr…
Comment: Metabat2 (binning package) Error: ReferenceFile: <filename>.fasta is not the sam
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Mensur Dlakic
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I don't mean to sound harsh, but this is pretty basic stuff that is easily resolved if you read through the CheckM2 manual and follow the d…
Comment: Metabat2 (binning package) Error: ReferenceFile: <filename>.fasta is not the sam
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samdegregori
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Yeah that's what I was thinking but triple checked and it seems to be right. And yes of course here is the output for reference:
runnin…
Comment: Interpreting Varied Survival Times in TCGA-BRCA Data
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Sorry for interrupting your question but can I ask you where you find the data on what samples belong to healthy patients and what sample t…
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I don't see why "samples with a survival outcome of 1" can't "have longer survival times than those where the survival outcome is 0"? Sampl…
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Oomycetes have pretty complex genomes (most of it repeats as I recall from working with one in distant past) so it would help a lot if you …
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I think the first part of your advice is on point. However, I don't see the logic with this part:
> One possible solution is to align all …
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There is a subset of BioPython called [**SeqIO**](https://biopython.org/wiki/SeqIO) with many examples of how to read and manipulate biolog…
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You can just concatenate the various R1 and R2 fastq files before running the assembly. Let's say you have two samples (sample1, sample2),…
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Python is not very efficient for that type of work. There are all kinds of existing tools that are much faster: BLAST, FASTA and DIAMOND ar…
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analyst
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Do you mean merging of fastq files and running assembly on merged fastq file?
For example for MaSuRCA I found following command that seems…
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If you have multiple samples from the same species, you can just combine the fastq files and generate a single assembly.
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