User: molly77

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molly7710
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Posts by molly77

<prev • 14 results • page 1 of 2 • next >
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tBLASTn - How do I turn all repetitive masking off??
... Hi, With tBLASTn v2.7.1+ on the command line: I'm using a transcriptome as my nucleotide database and using translated queries that are highly repetitive (these queries sequences have come from my transcriptome so I know they are there), and I'm not getting any hits. How do I go about generating h ...
assembly rna-seq blast tblastn written 10 days ago by molly7710
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Comment: C: tBLASTn - Warning: Could not calculate ungapped Karlin-Altschul parameters due t
... No non-standard characters, I have already troubleshooted for that. I believe it's because its highly repetitive (a Google search of the exact error message hints that it's because it's repetitive, but provides no other information). ...
written 10 days ago by molly7710
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tBLASTn - Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
... Hi, tBLASTn v2.7.1+ on the command line: I have a transcriptome as my nucleotide database and I am trying to identify repetitive fragments with translated repetitive queries. I have about ten different repetitive queries I am using, however, for two of them, I get the following error: "Warning: Co ...
software error alignment blast transcriptome written 11 days ago by molly7710
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Comment: C: Can I compare TPM values for a transcript across different transcriptome assembl
... Thank you to everyone who offered input, this was incredibly helpful in regard to the between experiment comparisons. However, I have another question in regard to the same gene expression analyses aforementioned, and I figure I'll post it here as a comment in the hopes you will offer additional ins ...
written 4 months ago by molly7710
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Can I compare TPM values for a transcript across different transcriptome assemblies?
... Hi, I have three transcriptome assemblies representing two different tissues from three different species within the same genus. Each transcriptome assembly consists of three biological replicates (two tissues from each individual, so six RNA-seq libraries per transcriptome assembly). I have Salmon ...
gene expression tpm rna-seq transcript written 4 months ago by molly7710
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Comment: C: Generate nucleotide multiple sequence alignment from protein alignment?
... Amazing. Thank you very much. ...
written 7 months ago by molly7710
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Generate nucleotide multiple sequence alignment from protein alignment?
... Hello, I am trying to generate multiple sequence alignments of N- and C-terminal domains (separately) from nucleotide sequences based on a sequence alignment of their encoded proteins. One of my issues is that not all of my nucleotide sequences start in the first codon position and many include eit ...
multiple sequence alignment written 7 months ago by molly7710 • updated 7 months ago by h.mon28k
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Best method to assemble low-abundance transcripts?
... Hi, There are a few parts to this post. I am determining the max or most optimal number of cDNA libraries I should add to an Illumina Nextseq flowcell (400M reads). I currently have 12 libraries, two different treatments per 3 different species and each sample has a biological replicate. This leave ...
assembly transcriptomics rna-seq illumina written 22 months ago by molly7710 • updated 22 months ago by Macspider3.0k
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Comment: C: Samtools stats output "reads mapped and paired"
... Thank you! However, I understand paired-end sequencing/reads and the reads mapped output, but I don't understand what the output for "reads mapped and paired" is. For example: sequences: 669518 reads mapped: 568365 reads mapped and paired: 494728 # paired-end technology bit set + both ...
written 2.2 years ago by molly7710 • updated 2.2 years ago by Pierre Lindenbaum124k
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Why does my genome annotation file contain only one type of feature? (i.e. mol_type=genomic DNA)
... Hi, I have a gff file of a genome that I obtained from NCBI. The gff file and corresponding genome fasta come from a recently published paper in Nature. However, the gff file only contains one type of feature, i.e. "genomic DNA". I don't receive any hits when I grep for gene or CDS etc. Why would t ...
genome annotation gff written 2.2 years ago by molly7710

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