User: max_19

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max_19110
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Posts by max_19

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Comment: C: Convert prodigal output
... This works perfectly - thank you! ...
written 21 days ago by max_19110
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Comment: C: Varying assembly statistics: Abyss & SPades
... Will try that - thank you! ...
written 4 weeks ago by max_19110
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Comment: C: Varying assembly statistics: Abyss & SPades
... I actually tried subsampling (Randomly select 15% of the data) and I assembled with SPades, see stats below: Assembly scaffolds # contigs (>= 0 bp) 12763 # contigs (>= 1000 bp) 1672 # contigs (>= 5000 bp) 87 # contigs ...
written 4 weeks ago by max_19110
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Comment: C: Varying assembly statistics: Abyss & SPades
... That is good to know, thank you! Expected assembly size is ~4.8MB. Adapters have been trimmed and I applied a quality filtering of q=30 with trimmomatic. Sequencing coverage is very high (~1000X). Once I remove those scaffolds that are very small from scaffolds.fasta, should I then remove the read ...
written 4 weeks ago by max_19110
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Comment: C: Varying assembly statistics: Abyss & SPades
... Thanks for your suggestion! I tried doing that and then running good_contigs.fa with QUAST, however the N50 did not change. Do you think I have to reassemble with SPades (i.e. remove all the reads which map to those contigs, then reassemble) ...
written 4 weeks ago by max_19110
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Comment: C: Searching and filtering uniclust databases
... Thanks for the helpful information! The uniclust download that I am using does not contain the **uniclust30_2018_08_consensus.fasta file** . I downloaded this one (uniclust30_2018_08_hhsuite.tar.gz) because I am using the database with HHsuite eventually. Here are the files that I have when I extr ...
written 3 months ago by max_19110
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Searching and filtering uniclust databases
... Hi there, Does anyone have experience with searching or filtering uniclust databases: http://gwdu111.gwdg.de/~compbiol/uniclust/2018_08/ For example if i want to search for a particular organism? or filter for only eukaryotes? (in the uniclust30db) I tried doing this with the mapping file that is ...
uniclust protein databases written 3 months ago by max_19110 • updated 3 months ago by SMK1.8k
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Comment: C: HH-suite: Segmentation fault (core dumped)
... I will try that instead! thanks for your help! ...
written 4 months ago by max_19110
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Comment: C: HH-suite: Segmentation fault (core dumped)
... I see. Each alignment is ~11,000 characters long. maybe there is a better way to go about this. I have 35 orthologous proteins (across 30 similar species) and i'd like to build an HMM profile with them and then compare them to HMM profiles in HH suite databases (profile vs profile), so I can determi ...
written 4 months ago by max_19110
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Comment: C: HH-suite: Segmentation fault (core dumped)
... Thanks for your help. I have to request memory allocations. I just ran it on a much smaller subset of my fasta file though, and the error persists. ...
written 4 months ago by max_19110

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