User: bioinfo17

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bioinfo1710
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Posts by bioinfo17

<prev • 28 results • page 1 of 3 • next >
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Comment: C: hisat2 parameters for paired end and single end reads from same samples
... Estimation of the insert size is a great idea. I will follow that. > Stringtie counts the number of reads that cover each position I have read the manual of stringtie but couldn't find an answer if it assembles transcripts based on both paired end and singletons reads and the counts generated w ...
written 9 weeks ago by bioinfo1710
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hisat2 parameters for paired end and single end reads from same samples
... Hi, I have paired end R1.fastq, R2.fastq and singletons.fastq files for the same samples. What parameters should I use for aligning reads against a genome of interest? 1) hisat2 -1 R1.fastq, -2 R2.fastq, -U singletons.fastq or just treat all the files as unpaired and use 2) hisat2 -U R1.fastq, ...
hisat stringtie alignment rna-seq hisat2 written 9 weeks ago by bioinfo1710 • updated 9 weeks ago by Macspider1.6k
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Comment: C: GMAP v2017-06-20 error
... Thanks, will do that. ...
written 4 months ago by bioinfo1710
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GMAP v2017-06-20 error
... Hi all, I am trying to align the de novo transcriptome (transcripts) against the reference genome via GMAP using the following command below: 1) have build a database of the genome using gmap-build command, 2) gmapl -D . -d database -2 genome_fasta trinity_fasta -f samse > trinity_gmap. ...
software error gmap alignment written 4 months ago by bioinfo1710 • updated 7 days ago by KVC_bioinfo200
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Comment: C: Aligning reads to genome together with transcriptome
... Hi EVR, What approach did you finally use for your analysis, would be really good to share? Thanks ...
written 4 months ago by bioinfo1710
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Comment: C: Hisat2 build index for genome + transcriptome files together
... Will give Salmon a try, thank you! ...
written 4 months ago by bioinfo1710
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Comment: C: Hisat2 build index for genome + transcriptome files together
... Thanks Devon for your quick reply. The % alignment rate was very low (~2-20%) when the sample reads were mapped against the individual genome fasta file, however, the alignment % significantly increased (~60-80%) when the sample reads were mapped against the transcriptome alone. I am unsure which on ...
written 4 months ago by bioinfo1710
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Hisat2 build index for genome + transcriptome files together
... Hi, Could anyone please explain how to use Hisat2 when both the genome and transcriptome is available for the same reference strain. The genome is annoated using maker and hence have the gene models in gff format. The transcriptome is also available but is present only as an assembled fasta format. ...
rna-seq written 4 months ago by bioinfo1710 • updated 4 months ago by Devon Ryan73k
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Comment: C: Augustus scipio error
... Hi, I think you just need to keep running it until you finish. I had to ignore the warnings. Even running scipio inside augustus gave me the same warnings. ...
written 6 months ago by bioinfo1710
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Comment: C: DESeq2 3-fatcor design and different interaction terms
... Hi, did you get the results what you were looking for? Would be great if you could please share how you have achieved your results. I'm currently using a similar experiment - thanks ...
written 6 months ago by bioinfo1710

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