Moderator: h.mon

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h.mon32k
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Posts by h.mon

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Comment: C: CD-HIT: representative sequence vs consensus sequence
... In the fast mode - which is the default - yes, that is precisely what is being done. In accurate mode, a sequence is compared to all representative sequences, and is added to the most similar one. From the [wiki][1]: > In default manner (fast mode), a query is grouped into the first representati ...
written 5 days ago by h.mon32k
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Comment: C: Error to use seqwish for multiple genomes
... I may be missing something, but I don't see `-k -B -P` at you pggb command-line. ...
written 6 days ago by h.mon32k
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Comment: C: CD-HIT: representative sequence vs consensus sequence
... As CD-HIT sorts and then processes the sequences from longest to shortest, it is both: each clusters representative sequence is both the longest for that cluster, and also the first to enter the cluster. ...
written 6 days ago by h.mon32k
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Comment: C: STAR --quantMode GeneCounts vs HTSeq-count
... Just go ahead with STAR counts. ...
written 9 days ago by h.mon32k
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Answer: A: Question about featureCounts strand options
... With paired-end reads, you should always use `-p`. It is really odd to get 70% assignment with `-s 0` and 0% with `-s 1` **and** `-s 2`. There is something funny either with your mapping or with your annotation. Is the annotation extremely compact, with all feature (genes) overlapping each other? ...
written 9 days ago by h.mon32k
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Answer: A: STAR --quantMode GeneCounts vs HTSeq-count
... The bellow is true for old versions of HTSeq-count, I believe it is still true for recent versions, but you should check the documentation. HTseq-count, by default, expects name-sorted bam files. If you use as input position-sorted bam files, HTSeq-count will not detect read pairs properly, and wil ...
written 9 days ago by h.mon32k
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Answer: A: Verification of successful engineering
... If you are engineering a bacteria, you are probably working with a single-isolate culture. Then, the complete workflow would be: sequence the original strain, sequence the putative transformed strain - best to sequence both with PacBio or Nanopore, assemble both genomes. Then there is a number of an ...
written 25 days ago by h.mon32k
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Comment: C: Is it possible to work with paired-end reads for assembly purposes using metaspa
... As https://www.biostars.org/u/78287/ stated bellow, the current (SPAdes 3.14.1) [manual][1] explicitly states for `--meta`, only one paired-end library can be used for assembly - that is, single-end libraries and / or multiple libraries are not supported: > --meta (same as metaspades.py) > ...
written 26 days ago by h.mon32k
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Comment: C: Large Count Discrepancy of Key Gene Between STAR and HISAT2
... You are confounding STAR mapping with STAR quantification (and mapping and quantification in general). STAR, in particular, only counts reads to genes if the reads can be unambiguously assigned to it. It may well be the case STAR mapped many reads to the gene in question, but counted 0 reads, becaus ...
written 26 days ago by h.mon32k
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Comment: C: Specific question on torturing the data until it confesses
... I agree with your first point. Nonetheless, I do find "biologically meaningful" useful, although dangerous. I didn't understand your second point. I partially agree with your third point, see my answer bellow. ...
written 26 days ago by h.mon32k

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