how_are_we_stranded_here
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signalbash
Check strandedness of RNA-Seq fastq files
Hello, I am getting an error while indexing of the BAM files. I have installed the tool using conda. So the kallisto version is at 0.44 as mentioned. Below is...
To whom it may concern, Hi! My name is Ryan Englander, I am an MD/PhD student at the Jackson Laboratory for Genomic Medicine. I am trying to use this package...
Apparently python does not like the line `result = pd.read_csv(test_folder + '/' + 'strandedness_check.txt', sep="\n", header=None)` anymore. Installing in a fresh conda env (with python 3.7) solved this. Error message:...
Hi, I tried to use how_are_we_stranded_here to figure out the strands of my RNA-seq data. Here are my commands: `check_strandedness --gtf Midas.annotation.v2.6.gtf -r1 Aast_14_trimmed_R1.fq.gz -r2 Aast_14_trimmed_R2.fq.gz -fa Midas.2.6.transcripts.fa` Here is...
In newer versions the python engine seems to have a problem with `\n` as separator or delimiter #14. Therefore, I propose another way of reading only the non-empty lines of...
Hi, I really want to try this package, but unfortunately I haven't been able to install it. I tried on a centos machine and an ubuntu machine, but in both...
I am trying to use your tool with GRCm39. I have been able to successfully build with m38, and GRCh38. However, for GRCm39 using ensembl v109, an error is thrown:...
# command check_strandedness --gtf /xxx/Mus_musculus.GRCm38.102.gtf --transcripts /xxx/Mus_musculus.GRCm38.dna.toplevel.fa SRR1538550.fastq.gz # log usage: check_strandedness [-h] -g GTF [-fa TRANSCRIPTS] [-n NREADS] -r1 READS_1 -r2 READS_2 [-k KALLISTO_INDEX] [-p] check_strandedness: error: the following...
Hello, I tried to get this tool running but encounter an issue. The following are the code and error messages that I got: Code: `check_strandedness --gtf ref/Mus_musculus.GRCm38.93.gtf --transcripts ref/Mus_musculus.GRCm38.cdna.all.fa --reads_1...
So using the latest version 0.46 (as well as version .45) of kallisto with how_are_we_stranded_here produces this error `stranded_test_gerald_H3MYFBBXX_1/kallisto_strand_test/pseudoalignments.bam does NOT exists. Traceback (most recent call last): File "/usr/local/bin/check_strandedness", line...
