User: gwrathe

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gwrathe0
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Posts by gwrathe

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Comment: C: Mothur: following SOP, received a weird alignment, screen.seqs failing
... Renamed output of pcr.seqs. [mothur > rename.file(input=silva.nr_v132.pcr.align, new=silva.v4.fasta)]. I realise the '4' is for the primer region used in the SOP and I just didn't change it, should just be a name and have no effect on the file contents. Sorry for being unclear earlier. ...
written 8 weeks ago by gwrathe0
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Comment: C: Mothur: following SOP, received a weird alignment, screen.seqs failing
... I downloaded the silva.nr_v132.align file and used pcr.seqs with my primer start and end points. I used the output as the align.seqs reference file. ...
written 8 weeks ago by gwrathe0
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Mothur: following SOP, received a weird alignment, screen.seqs failing
... Hello, I've been running through the Mothur SOP almost character for character with the V1-V3 region 27f/519r, start = 1046, end = 13127 primers. I hit the following error message when I ran the 'screen.seqs' command after my alignment. Running command: remove.seqs(accnos=stability.trim.cont ...
miseq mothur alignment silva sequencing written 8 weeks ago by gwrathe0
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Comment: C: Diamond results non-specific compared to NCBI Web
... Thank you buchfink! Much appreciated. ...
written 11 weeks ago by gwrathe0
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Diamond results non-specific compared to NCBI Web
... Hello, I recently downloaded and set up the nr database from NCBI using Diamond. I ran my sequences through using the taxonomic information tags. Using the following command lines: > diamond makedb --in nr.gz --taxonmap prot.accession2taxid.gz --taxonnodes nodes.dmp -d nr > diamond blastp -d ...
ncbi blast diamond blastp written 11 weeks ago by gwrathe0 • updated 11 weeks ago by buchfink140
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How to identify best-hit taxonomy of many gene sequences efficently
... Hello, I have many sequences, each represents a species. I have the aim of identifying these sequences using their best-hit and recording that information to find the relative diversity of my community. I could go on to NCBI refseq and grab the best-hit for each of my sequences and record them but t ...
gene sequence taxonomy ncbi written 3 months ago by gwrathe0

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