User: cschu181
cschu181 • 2.5k
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Posts by cschu181
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Comment:
C: Setting up BUSCO well
... https://gitlab.com/ezlab/busco/-/issues/342 ...
written 2 days ago by
cschu181 • 2.5k
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... Indeed, instead of the `return False` you'd `raise BadSequenceException(x + " is not a valid nucleobase")` (or something like that).
In addition to that, do you really want to add the empty sequence (upon encountering the first sequence header `>`) to the set of sequences? ...
written 4 days ago by
cschu181 • 2.5k
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Comment:
C: Setting up BUSCO well
... OP needs to be careful, though, what a successful testrun means. With a previous BUSCO version, I once had the .odb databases unreachable due to filesystem permissions. Did that stop BUSCO from running? No, it just ran everything against the integrated mouse (I think it was mouse) database. It repor ...
written 4 days ago by
cschu181 • 2.5k
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... The general recipe (with a couple hints) for this is:
1. Change your sequence into a list of characters `seq = list(seq)`
2. Fill a dictionary with the replacements that you want to do, e.g.
`repl = {"UCA": ["UCU", "UCG", "UCC"] , ... }`
3. Iterate over your sequence in substrings of 3 (=cod ...
written 5 days ago by
cschu181 • 2.5k
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Comment:
C: repeating bwa alignment
... If I remember correctly, bwa aln needs to be followed by bwa sampe (for paired) bwa samse (for single-end). I assume, the bam files you have, are actually sai files. Furthermore, your command doesn't make sense as you have the `-o` switch twice, once for gap open (the right switch for bwa aln) and o ...
written 6 weeks ago by
cschu181 • 2.5k
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Comment:
C: Error: Empty BAM file in DANPOS3
... Given the horrible implementation of DANPOS I wouldn't be surprised if that was actually the case.. ...
written 7 weeks ago by
cschu181 • 2.5k
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Comment:
C: Error: Empty BAM file in DANPOS3
... I'd post DANPOS3 issues directly to the dev's github: https://github.com/sklasfeld/DANPOS3/issues. DANPOS3 is a Python3 port of DANPOS/2, but from a 3rd party dev. The port has/used to have some issues, maybe this is one of them. ...
written 7 weeks ago by
cschu181 • 2.5k
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... I think you could use sortmerna, which is used to filter rrna from rna-seq, but since rna-seq is cdna, I assume the tool should be applicable to dna reads as well. ...
written 7 weeks ago by
cschu181 • 2.5k
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Comment:
C: Manually Search Sam/Bam File
... > so I tried blasting
With small reads, you're better (and faster) off to use an aligner/mapper such as bwa or bowtie(2). ...
written 7 weeks ago by
cschu181 • 2.5k
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... First, I assume your reads are Illumina?
Is there a reason why you're BLATing such small reads and not use a read mapper (bwa/bowtie(2))?
By limiting to exact matches, you will not get any variant position (since you're filtering them out). I'd use one of the read mappers I mentioned. Since these ar ...
written 7 weeks ago by
cschu181 • 2.5k
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