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Hello,
I am working with bulk RNA seq data. I created a reference like shown below:
`kallisto index -i mouse_version111cdna Mus_musculus.GRCm39.cdna.all.fa.gz`
Then I created a t2g file using…
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When converting c. HGVS from cDNA to genome coordinates, VEP appears to not take into account alignment gaps, where the cDNA has insertions/deletions vs the reference sequence.
Submission example:
…
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Hello,
I have leukemia samples sequenced by cDNA-ONT, I would like to know if it is possible to run ALLsorts to predict ALL subtypte. Have you ever tried it?
Thank you,
Maria Sol
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The reference creation process breaks:
docker run -v /mnt/morris/defuse/:/data jeltje/defuse reference -c hg38config.txt
...
Input files DNA, FASTA:
/data/defuseData/defuse.cdna.fa
…
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I used cDNA_MINES.py command and it gives me following error with command-
python /home/aclab/apps/MINES/cDNA_MINES.py --fraction_modified control.fraction_modified_reads.plus.wig.bed --coverage con…
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Process variant with this cdna:
`NM_015074.3:c.184-7_184-6del, NM_183416.3:c.184-7_184-6del`
Expected:
cDNA is `c.184-7_184-6del` in output
Observed:
cDNA is `c.184-7_184-6del, NM_183416.3`…
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Hi,
I have questions about fragment size using short read data. When I analyzed short read paired Illumina RNA data, the RPVG estimated the fragment distribution with a mean of 181.201 and a standa…
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We would like to use Dorado polyA estimation for our custom cDNA method called Nano3Pseq, which uses NBD114 kit. The adapter sequence is similar to the VNP oligo used for cDNA synthesis.
Thanks,
…
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Hi,
First of all, we want to thank you for this wonderful application. It has streamlined our variant annotation workflow tremendously.
We submitted the HG19 chr16-11349332-CC-TT variant to Ope…
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### Ask away!
The PCR-cDNA barcoding kit, incorporates UMIs with the strand switching primer into the strands which are then sequenced. Is there a point in this pipeline that takes these UMIs into ac…