User: LAB_2019

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LAB_20190
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Posts by LAB_2019

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Intron finder for 3' UTR sequences (non-model organism)?
... Thanks for the advice. My organism does have NMD, so I do expect that 3' UTRs with introns would be degraded, but I'm hoping to still detect some (NMD is not 100% efficient). In reference to your first question. The GFF file seems to have only introns annotated that were in the ORF, as I could not ...
written 10 months ago by LAB_20190
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Intron finder for 3' UTR sequences (non-model organism)?
... I am trying to find introns retained in 3' UTR sequences. I have FASTA files for both the entire transcriptome & just the 3' UTR sequences for each transcript. Is there any software that can map introns using either FASTA file (preferably the 3' UTR.fa file)? The GFF file I have contains annot ...
sequence alignment rna-seq written 11 months ago by LAB_20190
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Comment: C: No aligned reads after featurecounts. BAM files have >85% reads mapped
... Thanks for pointing this out. I repeated my analysis using Salmon. Overall, the general trends seem highly similar, but this is definitely a more accurate approach. ...
written 11 months ago by LAB_20190
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Comment: C: No aligned reads after featurecounts. BAM files have >85% reads mapped
... Thanks for your help. I think I accomplished what I needed to do with your suggestions. Here is what I did: 1. Mapped reads w/ HISAT2 to transcripts.fa 2. Performed idxStats on .BAM files to count #mapped reads 3. Constructed raw counts file and performed differential gene expression analysis The ...
written 11 months ago by LAB_20190
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Comment: C: No aligned reads after featurecounts. BAM files have >85% reads mapped
... I simplified this. I re-ran HISAT2 with my paired-end fastq files and only the transcripts.fa file as a reference. here is the format of the transcripts.fa >Niben101Scf03546g00006.1 TTTTTAAATATTAAATTCATAAAATTTAGA This produced the .BAM file. Here is a sample for idxStats (had ~65% mappe ...
written 11 months ago by LAB_20190
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Comment: C: No aligned reads after featurecounts. BAM files have >85% reads mapped
... Thanks for the advice. I am going to re-align one test sample using only 1 .fa file. I will double check the Genome.fa and transcripts.fa to make sure they have the same ID's as my .GFF file. I am mainly trying to differential gene expression analysis. Would you recommend using only the transcripts. ...
written 11 months ago by LAB_20190
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Comment: C: No aligned reads after featurecounts. BAM files have >85% reads mapped
... The BAM files were generated using a "contigs" .fasta and a "transcripts" .fasta. The transcript format wasx as such: Niben101_annotation.transcripts.fasta >Niben101Scf03546g00006.1 TTTTTAAATATTAAATTCATAAAATTTAGACCTGG Is there a way to edit the BAM or .GFF files to create uniformity ...
written 11 months ago by LAB_20190
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No aligned reads after featurecounts. BAM files have >85% reads mapped
... Hello, new to RNA-seq here. I have mapped my fastq reads to a reference genome (transcript.fasta) with HISAT2. The BAM files look very good with >85% reads mapped. However, when I try to use featurecounts, both local and on Galaxy, the results always yield 0 mapped reads. From lurking around the ...
rna-seq written 11 months ago by LAB_20190 • updated 11 months ago by lieven.sterck7.8k

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