User: cschu181
cschu181 • 2.3k
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Posts by cschu181
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... If you can use short-blastn instead of megablast in the "browser version" (assuming blast.ncbi.nlm.nih.gov?), then it might work, but as Pierre says, it might be too short and degenerate. ...
written 3 days ago by
cschu181 • 2.3k
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... Filter the low quality reads, i.e. if the average quality of the whole read is lower than a certain threshold, then discard it. I would only trim low quality of phred < 3, i.e. the everything the sequencer labels as garbage and then do a length filtering. The more bases you trim off, the more lik ...
written 3 days ago by
cschu181 • 2.3k
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... `{sample}` and `{sample}.gz` still use the same `{sample}` wildcard. In your case, `{sample}` is the whole filename, but in theory, you could also construct a filename like `/path/to/file/{sample}_R1.fastq.gz`, with `{sample}` only storing the file prefix. It depends how you intend to process your d ...
written 7 days ago by
cschu181 • 2.3k
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... I'm not sure that it would add more wildcards. However, you need to differentiate between files that need to be gzipped and files that don't. From my experience with routing different sample types (I didn't have the zipped/non-zipped problem, but I have had single-end vs paired end and even RNAseq v ...
written 8 days ago by
cschu181 • 2.3k
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... Both work, yes, but `== True` (or `!= True` or ... ) is considered "bad practice". Just pointing it out. ...
written 8 days ago by
cschu181 • 2.3k
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... Additionally,
if wildcards.sample.endswith('.fastq') == True:
should be:
if wildcards.sample.endswith('.fastq'): ...
written 9 days ago by
cschu181 • 2.3k
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... I don't know pandas (seems to be overkill to use this for parsing a simple two-column table), but can you add a filter to
expand(SCRATCH + "/02ZIPPED_fqs/{sample}", sample = sample_df.sampleID
so that you will only have the unzipped fastqs in `sample`?
And then I'd add the `.gz` extension to ...
written 9 days ago by
cschu181 • 2.3k
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... Just to ensure: there is actual output in the blastresults.txt? ...
written 9 days ago by
cschu181 • 2.3k
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... cat *_1.fastq > concatenated_1.fastq
cat *_2.fastq > concatenated_2.fastq
should do it
...
written 9 days ago by
cschu181 • 2.3k
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... Ok, while I agree that you should probably use `bedtools intersect`, I am always happy to see that people like to learn how things work. So, here's what comes to mind in your script:
1. You're storing everything from file2 in a dictionary, which you only iterate over once. You could easily merge bl ...
written 10 days ago by
cschu181 • 2.3k
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