User: dimitrischat

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dimitrischat100
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Posts by dimitrischat

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Trinity transcript_abundance.pl error using RSEM
... when i try to run transcript_abundance.pl using RSEM ./align_and_estimate_abundance.pl --seqType fq --single '..x.fastq' --transcripts '.../Trinity.fasta' --output_dir '/..output' --est_method RSEM --aln_method bowtie2 --trinity_mode --prep_reference it runs good up until : samtools sor ...
assembly rna-seq written 7 days ago by dimitrischat100
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Comment: C: RSEM: transcripts.fa.grp not found (should it have been generated?)
... could you explain a bit more how you did it? instead of lets say --transcripts xx.fasta , you did what? ...
written 7 days ago by dimitrischat100
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Comment: C: hmmscan using Pfam databases
... what do you mean by that "as Pfam is organized in terms of protein domains, it may well be there is no domain exclusive to the above search terms. If this is the case, the Pfam error message could be improved." ? ...
written 13 days ago by dimitrischat100
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Comment: C: hmmscan using Pfam databases
... Thanks a lot for your help. Unfortunately i get the same error when toggling the "..unique.." option. I contacted them via email, hope they reply. ...
written 14 days ago by dimitrischat100
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hmmscan using Pfam databases
... Hello, wanted to ask if you could do a specific search using pfam databases, f.e. plants ( taxid: 33090 )? Thanks hmmscan --cpu 8 --domtblout pfam.domtblout /path/to/Pfam-A.hmm transdecoder_dir/longest_orfs.pep edit: or maybe i could edit the database Pfam-A.hmm and keep only taxonomy 33090 ...
rna-seq written 14 days ago by dimitrischat100
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Comment: C: how to get database of plants in FASTA format from uniprot
... yea dont know if you can use them (.dat files) for blastp in terminal. Or you can? edit: is there a way to convert .dat file to .fasta ? ...
written 14 days ago by dimitrischat100
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Comment: C: how to get database of plants in FASTA format from uniprot
... but this is .dat file not fasta ...
written 14 days ago by dimitrischat100
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Comment: C: Restricting database by taxa in local blast searches
... using as database the uniprot_sprot.fasta, can i use the -taxidlist plants.ids ( sh get_species_taxids.sh -t 33090 > plants.ids ) ? or it doesnt make any sense? And if i cant, how can i do that with the uniprot_sprot database? ...
written 14 days ago by dimitrischat100
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De novo transcriptome assembly, annotation, blast using Trinity, transdecoder and blast
... Hello all, never done this before so i will need some guidelines. I am trying to do a de novo transcriptome assembly from a single rna-seq fastq file using Trinity (trimming makes a difference or no?). After 18h it produced a lot of files but i am guessing the one i want is the Trinity.fasta. After ...
assembly rna-seq written 15 days ago by dimitrischat100 • updated 14 days ago by h.mon29k
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Comment: C: Restricting database by taxa in local blast searches
... i got nr00 up to nr38, all files about ~200gb. I need all right? i mean when i use -db ../ncbi_blast_database/nr , it searches all? but with -taxidlist it searches only this taxa within all nr files? ...
written 15 days ago by dimitrischat100

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