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lr-kallisto quantification #469

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AhmedSAHassan opened this issue Dec 6, 2024 · 0 comments
Open

lr-kallisto quantification #469

AhmedSAHassan opened this issue Dec 6, 2024 · 0 comments

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@AhmedSAHassan
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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.

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