User: molly77

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molly7710
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m***********@student.uml.edu

Posts by molly77

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Generate nucleotide multiple sequence alignment from protein alignment?
... Amazing. Thank you very much. ...
written 10 days 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 13 days ago by molly7710 • updated 12 days ago by h.mon25k
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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 15 months ago by molly7710 • updated 15 months ago by Macspider2.8k
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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 19 months ago by molly7710 • updated 19 months ago by Pierre Lindenbaum120k
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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 19 months ago by molly7710
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Comment: A: Get cds using bedtools
... Do I have to modify my gff file to extract only CDS from my genome fasta? The bedtools getfasta manual is not informative to me. ...
written 19 months ago by molly7710
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Comment: C: Get cds using bedtools
... Hi, I am also trying to use bedtools to extract CDS from a genome fasta. However, I don't undertstand what the bed file is? Do I have to modify my gff file to only contain the hits of CDS? ...
written 19 months ago by molly7710
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Comment: C: Program that will extract all CDS from protein-coding genes in a genome fasta fi
... Hi Kevin, Thank you for responding. I tried gffread but didn't have any luck for some unknown reason. I built an index of my genome with Samtools and made sure that the index was in the same directory as my genome (I used the -g flag) and full path to the genome as well as the gff file, but I recei ...
written 19 months ago by molly7710
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Program that will extract all CDS from protein-coding genes in a genome fasta file (with gff file)
... Hi, I have a genome fasta file and corresponding gff annotation file, how can I extract all CDS from all of the protein-coding genes in the genome? I would prefer to use an actual program rather than a script to do this, as I would have a harder time modifying/troubleshooting a script than using a ...
genome gene cds written 19 months ago by molly7710 • updated 19 months ago by Kevin Blighe42k

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