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We observed that in the **metrics_summary.xls** file under **04.report**, the cDNA Number of reads is **1,858,750,737**, but in the **anno_decon_sorted.bam** file under the **output** directory, there…
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Hi,
Hope that seqkit can extract transrcipt/cdna/gene/protein sequences from references fasta and gff/gtf file. gffread can do this but it can not handle large chromosomes correctly.
Best,
Kun
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Hello,
Thanks very much for this tool! Are you planning to add a model for R10 cDNA any time soon? I suspect that it would get a lot of use.
Thanks,
John
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**User story**
As a member of the SSR team, who has received a plate from faculty containing cDNA, I would like to be able to import them into Sequencescape along with all the required data.
**Who…
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Hi Zhenyu，
I noticed in the script S02.umi.process.one.sh, you used minimap2 for mapping to the reference genome and then used salmon for quantification. Additionally, it seems that for the referen…
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https://asia.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000136250;r=7:36512941-36724494;t=ENST00000617537
Web page Reports that the sequence is 2385 bases long
Ensembl API is in…
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I am using singularity to run this pipeline.
Unable to download requested sequence data from Ensembl (ftp://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.…
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Thank you for sharing your code and data :)
However, I encountered an issue while examining the cDNA data. I noticed that several PDB entries, which provide corresponding MSAs and FASTA files, are n…
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Hello, I'm sorry to bother you. May I know how to do transcriptome prediction now that I only have full-length transcriptome data?
I have seen many articles on downstreaming the data and then using …
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Hello,
Can the same pipeline be used for cDNA sequencing as well? I have the fastq reads and the reference genome and transcriptome fasta sequences.
Thank you.