User: nancydong20

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nancydong2060
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Posts by nancydong20

<prev • 32 results • page 1 of 4 • next >
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RepeatModeler and RepeatMasker for non-model species
... Hello everyone! I am trying to analyze repeat elements in a new draft genome of a non-model organism. I used RepeatModeler to build a *de novo* repeat library, and then used RepeatMasker (rmblastn version 2.2.27+) to mask the genome. In the .tbl output, I see that no simple repeats or low complexi ...
repeatmasker repeatmodeler written 7 days ago by nancydong2060
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Comment: C: A question about Perl symbol lookup error
... Okay sure, thank you very much for letting me know! ...
written 12 days ago by nancydong2060
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(Closed) A question about Perl symbol lookup error
... Hello everyone! I installed several Perl modules in a local library on a cluster, since I don't have root access. After this, even though the program that uses these Perl modules seems to run without problem, I get this error message in the first line of the log that I get upon completion of each j ...
perl written 12 days ago by nancydong2060
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Comment: C: Should RNA-seq data be assembled before analyzing?
... Thank you very much for your reply! There is a draft genome for this organism, but it's only on its first release. I worry that by aligning the reads to a maybe not-so-accurate genome can cause me to lose out on useful information in the transcriptome? ...
written 4 weeks ago by nancydong2060
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Should RNA-seq data be assembled before analyzing?
... Hello! Should RNA-seq data (almost) always be assembled first into contigs before analyzing? From what I can see, not all published transcriptome studies assemble the reads before proceeding onto expression level analysis. My understanding is that assembling into contigs will enable better ORF/ge ...
assembly rna-seq written 4 weeks ago by nancydong2060
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Comment: C: Zero length branches on a phylogram
... Thank you very much! ...
written 5 weeks ago by nancydong2060
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Comment: C: Zero length branches on a phylogram
... Thank you very much for the quick reply! I am comparing the sequences of a single protein across species, so unfortunately I don't know how I can use data with more divergence? ...
written 6 weeks ago by nancydong2060
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Zero length branches on a phylogram
... Hello everyone! I am currently comparing the orthologs of a single protein, doing multiple alignments and constructing a phylogram using MEGA7. I am seeing several zero-length branches (three out of seven branches). I search around online and see that this is assumed to be because the "descendants" ...
mega7 phylogenetic tree written 6 weeks ago by nancydong2060 • updated 6 weeks ago by Sergey Naumenko170
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Comment: C: Ways to merge GO terms from different analyses?
... I'm sorry for the late reply, and thank you very much for the suggestion! After looking at Trinotate, I see that it handles transcriptome data? What I have is the proteome set from a new genome, and would like to analyze at the protein level. Is there a program that can be recommended for that? ...
written 11 weeks ago by nancydong2060
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Ways to merge GO terms from different analyses?
... Hello! I would like to do gene ontology annotation of a set of proteins from a non-model organism. I have been using BLAST2GO, mainly because it allows me to merge GO terms from the "mapping" step with those from InterProScan quite easily. However, it conducts web-based InterProScan and so is very ...
gene ontology written 12 weeks ago by nancydong2060 • updated 12 weeks ago by Whoknows580

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