-
Hi
I am getting an error:
make: *** No rule to make target 'sheep/data/Ovis_aries.Oar_v3.1.88.chr.gtf.mapTrans2Gene.tsv', needed by 'sheep/star/cufflinks2//pt0a.se.transcripts.riu.cufflinks2.ir…
-
Hi Rob and team.
I am obtaining the following errors in some of my samples but not all and I cannot figure out what is happening.
I am using salmon to see if specific genes are present (apart fr…
-
Finally able to install `sleuth` (had to reinstall `Rcpp`...), I'm trying out the vingette but getting stuck. I'm reading it from this [`Rmd`](https://github.com/pachterlab/sleuth/blob/master/vignette…
-
Can you possibly add a template for a PairedEnd RNAseq experiment?
And a single end alignment using the genome file that has the ERCC spike ins appended?
Also would it be possible toupdate the cur…
-
SuRE-seq, the previous dataset I was working with, is fundamentally a promoter assay, and therefore it was hard to find many biologically relevant features other than GC content (which affects nucleos…
-
Hi,
I am trying to mimic the steps of ExpressionAtlas pipeline, of experiment [E-MTAB-2836](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-2836/analysis-methods) . To try it out I came up with the foll…
-
Hi Rob,
I'm going to be running Salmon on some samples that were multiplexed during sequencing, i.e. each replicate has > 1 pair of FASTQ files. My instinct is that I should concatenate each of R1 and…
-
Hi,
I'm trying to run Sailfish + Rapclust in my data. I had some RNAseq samples from several conditions and I assembled with Trinity each condition separately, obtaining 4 different transcriptomes. No…
-
I've just been testing Salmon using Illumina TruSeq stranded (dUTP) libraries. Using either `ISF` (correct libType) or `ISR` I get a **ton** of messages like this:
```
expected = Library format { typ…
-
I tried to run kallisto but get followling error. I need a help
prabinb@biolab:/data/Prabin_trinity/Jonsok_complete_trinity> /data/trinityrnaseq-2.1.1/util/align_and_estimate_abundance.pl --transcrip…