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Hello,
I am using kallisto on my ONT cDNA bulk seq data.
The est.counts and tpm columns in the abundance.gene_1.tsv file are Zero for all the transcripts.
Is there something wrong that you can spot here?
I have used the following code to build the index and for quantification.
" kallisto index -i index.idx reference/gencode.v47.transcripts.fa.gz
For sample in FASTQ/*.fastq-gz; do sample_name=$(basename "$sample" ".fastq.gz") echo "Working on $sample..." mkdir -p kallisto_out/"$sample_name"/ kallisto bus -t 12 --long --threshold 0.8 -x bulk -i reference/index.idx -o kallisto_out/"$sample_name"/ -G reference/gencode.v47.annotation.gtf "$sample" done
for sample in kallisto_out/PAU*/;do bustools sort -t 12 "$sample"/output.bus -o "$sample"/sorted.bus done
for sample in kallisto_out/PAU*/;do bustools count "$sample"/sorted.bus -t "$sample"/transcripts.txt -e "$sample"/matrix.ec -g reference/gencode.v47.annotation.gtf -o "$sample"/count --cm -m done
for sample in kallisto_out/PAU*/;do kallisto quant-tcc -t 12 --long -P ONT -f "$sample"/flens.txt -i reference/ref_index -e "$sample"/count.ec.txt -G reference/gencode.v47.annotation.gtf -o "$sample"/quant-tcc --matrix-to-files "$sample"/count.mtx done "
Thanks in advance.
The text was updated successfully, but these errors were encountered:
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Hello,
I am using kallisto on my ONT cDNA bulk seq data.
The est.counts and tpm columns in the abundance.gene_1.tsv file are Zero for all the transcripts.
Is there something wrong that you can spot here?
I have used the following code to build the index and for quantification.
"
kallisto index -i index.idx reference/gencode.v47.transcripts.fa.gz
For sample in FASTQ/*.fastq-gz; do
sample_name=$(basename "$sample" ".fastq.gz")
echo "Working on $sample..."
mkdir -p kallisto_out/"$sample_name"/
kallisto bus -t 12 --long --threshold 0.8 -x bulk -i reference/index.idx
-o kallisto_out/"$sample_name"/ -G reference/gencode.v47.annotation.gtf "$sample"
done
for sample in kallisto_out/PAU*/;do
bustools sort -t 12 "$sample"/output.bus
-o "$sample"/sorted.bus
done
for sample in kallisto_out/PAU*/;do
bustools count "$sample"/sorted.bus
-t "$sample"/transcripts.txt
-e "$sample"/matrix.ec
-g reference/gencode.v47.annotation.gtf
-o "$sample"/count --cm -m
done
for sample in kallisto_out/PAU*/;do
kallisto quant-tcc -t 12
--long -P ONT
-f "$sample"/flens.txt
-i reference/ref_index
-e "$sample"/count.ec.txt
-G reference/gencode.v47.annotation.gtf
-o "$sample"/quant-tcc
--matrix-to-files
"$sample"/count.mtx
done
"
Thanks in advance.
The text was updated successfully, but these errors were encountered: