User: lagartija

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lagartija60
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Posts by lagartija

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test significance of species abundance in metagenomic data
... Hi there, I wondered which non parametrical test I can use to test if my samples are different in their species abundance. I have an abundance table (sum of coverages for each group) of all my samples. I tried using a friedman test but the results are quite weird. Thank you very much. Cheers, ...
metagenomics ecology written 10 weeks ago by lagartija60
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psiblast to get pssm. How to get a pssm from a multiple alignment ?
... Hi, I have problems using psiblast this being my command line : psiblast -subject test.fa -in_msa aligment_test.fa -out_ascii_pssm pssm_test1.txt -ignore_msa_master I get this error message whenever I have more that 4 sequences : BLAST options error: Repeated Seq-IDs detected in multiple seq ...
pssm written 4 months ago by lagartija60 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: How To Create A Pssm From Fasta Homologues With Ncbi Blast+ 2.2.23
... I think you should use the -ignore_msa_master option https://www.ncbi.nlm.nih.gov/books/NBK279694/ ...
written 4 months ago by lagartija60
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Comment: C: Mapping of metagenomic reads on genomes - length criteria ?
... The reason that I thought about removing short reads is to get less false positives. I looked at the first alignments and saw that most of the matches were short reads, often with repeats. I thought that if only short reads are matching, it might be only false positives. ...
written 4 months ago by lagartija60
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Mapping of metagenomic reads on genomes - length criteria ?
... Hi, I am mapping reads to genomes to estimate their abundance in several metagenomic samples. My problem is that when I filter for reads that are over 33 nt long I get a complete different result than when I keep all the reads. Which criterias should I apply to do the mapping ? Thank you very mu ...
mapping written 4 months ago by lagartija60
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Answer: A: Question about shotgun Metagenomic
... Hi, qiime works, I don't know about Mothur. You can also use kraken, kaiju, MG-RAST. It depends on what do you whant to do ! ...
written 4 months ago by lagartija60
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pssm for rpsblast
... Hi, I'm trying to make a database for rpsblast but I don't know how to create a pssm for the database. I have an alignment in fasta format : https://prosite.expasy.org/cgi-bin/aligner?psa=PS50104&format=FASTA and I can also get more information about this domain on prosite : https://prosite.e ...
domains written 5 months ago by lagartija60
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Answer: A: Relative abundance fro metagenomics samples
... Hi, I'm found this post useful because I have the same task (exept that I prefere to work on contigs than on bins). I also mapped the reads to my contigs to get the mean coverage. Is that a sufficient estimation of the (relative) abundance or do I have more steps to do to reduce biases ? ...
written 5 months ago by lagartija60
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Comment: C: running BUSCO on unknown genomes ?
... Thank you for your answer. I think the default parameter is the fruit fly. Can I avoid orfing by augustus somehow ? ...
written 6 months ago by lagartija60
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running BUSCO on unknown genomes ?
... Hi, I'm trying to assess my genome completeness and possible contamination with busco. Is it possible to run it several files at the same time ? Is it also possible not to use a reference species when orfing with augustus while running BUSCO ? I am trying to find an equivalent to checkm but for e ...
assembly written 6 months ago by lagartija60 • updated 6 months ago by Corentin380

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