User: amy.bashir

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amy.bashir80
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Posts by amy.bashir

<prev • 20 results • page 2 of 2 • next >
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Answer: A: Breakdancer : Can't locate Statistics/Descriptive.pm in @INC while trying to run
... I remember having a similar problem, it was because I had two versions of Perl installed so the paths got all messed up. Is the Statistics/Descriptive module in one of the paths listed in @INC: /usr/local/lib64/perl5 OR /usr/local/share/perl5 OR /usr/lib64/perl5/vendor_perl OR /usr/share/perl5/ve ...
written 2.8 years ago by amy.bashir80
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Hello, As you recommended, I tried this command to prepare the goa_uniprot_all database: nohup ./prepare_database -db=GO_all -org=goa_uniprot_all & I also tried to use "update" mode along with a gene list, but in both cases, I see that the database files get stuck in the state as shown i ...
written 2.8 years ago by amy.bashir80
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Comment: C: Are TPM values generated by different programs comparable?
... Oh, that's a great idea. Thank you very much! ...
written 2.8 years ago by amy.bashir80
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Are TPM values generated by different programs comparable?
... Hello! I am currently analyzing a set of RNA-seq data. I first used StringTie to calculate the TPM values of reads that are mapped to the genome (a non-model organism). Then, for the ~5% of reads that were not mapped to the genome, I used Trinity to *de novo* assemble the reads and then used Kallis ...
stringtie tpm kallisto written 2.8 years ago by amy.bashir80 • updated 2.8 years ago by h.mon30k
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Great, thank you very much, I am trying that now! ...
written 2.9 years ago by amy.bashir80
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Hello! I started the prepare_database job for goa_uniprot_all about 9 hours ago when I saw your answer. This is the command I used: nohup ./prepare_database -db=GO_BP -org=goa_uniprot_all The database seems to have been downloaded without problem, but it's been stuck without any change after ...
written 2.9 years ago by amy.bashir80
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Thank you very much for your quick reply! I will try that! ...
written 2.9 years ago by amy.bashir80
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Comment: A: Gene Set Clustering based on Functional annotation (GeneSCF)
... Hello! Thank you very much for making geneSCF, it works really well! I am currently trying to prepare the "goa_uniprot_all" database, which is quite large. I tried a few times before using a cluster, but the job could not finish for a long time. Do you have an estimated time for how long it would ...
written 2.9 years ago by amy.bashir80
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Comment: C: Workflow for annotating repeat elements
... I saw that RepeatModeler uses Trf, but I got 0% for "simple repeats" and "low complexity", so I wondered if I do Trf analysis separately, I might see something different. I am doing the repeat element annotation to see what percentage of the genome is repeat sequences, not to mask the sequence. ...
written 2.9 years ago by amy.bashir80
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Workflow for annotating repeat elements
... Hello everyone! I am doing repeat elements annotation for a new genome. From what I read online and in papers, the work flow is 1) Dustmasker, 2) Trf, 3) RepeatModeler and 4) RepeatMasker. I just finished masking the low complexity regions using Dustmasker. Should I use the hard masked file as inp ...
repeat elements written 2.9 years ago by amy.bashir80

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Scholar 2.8 years ago, created an answer that has been accepted. For A: WGCNA analysis for normalised data expression data sets

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