User: molly77

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molly7710
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Posts by molly77

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Append TPM value to sequence header in FASTA file
... The format keeps getting messed up when trying to add example. But I have one file with two columns. Transcript IDs in column 1, TPM value in column 2. My transcriptome FASTA file IDs for example ">TRINITY_1" (followed by the sequence on the next line) but I want the TPM value appended so "> ...
written 9 months ago by molly7710
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Append TPM value to sequence header in FASTA file
... Hi, I have TPM values for every transcript in my transcriptome. I want to append the TPM value of each transcript to its corresponding sequence header in the transcriptome FASTA file. For example, I have a file where column one lists each transcript sequence ID and then column two lists the TPM val ...
fasta tpm rna-seq transcripts linux written 9 months ago by molly7710 • updated 9 months ago by JC12k
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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 12 months 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 12 months 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 12 months 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 16 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 16 months ago by molly7710
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Comment: C: Generate nucleotide multiple sequence alignment from protein alignment?
... Amazing. Thank you very much. ...
written 18 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 19 months ago by molly7710 • updated 19 months ago by h.mon31k
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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 2.8 years ago by molly7710 • updated 2.8 years ago by Macspider3.3k

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