Activity for cash-program
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Alexander Pertovich Rezvykh posted a comment on discussion General Discussion
Hello! I've tried CASH for detecting and categorizing alternative splicing events in mice. But, output table contains gene names (such as Ndrg3, Nrcam and others), but there are no names of spliced transcripts. Is there a way to count splice events not for genes, but for each transcript (in Ensembl annotation GTF they are named as ENSMUST00000161639, ENSMUST00000074846)? Thanks !
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cash-program released /2.2.1/cash_v2.2.1.zip
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Andrew Lang posted a comment on discussion General Discussion
I have been attempting to use CASH to analyze a dataset for alternative splicing, but I am having difficulty getting the program to even read in my gtf. [al2025@premise isoform]$ java -jar -Xmx900m /pylon2/mc3bg6p/al2025/storage/cash_v2.1.0-alpha1/cash.jar \ > --Case:stress /mnt/lustre/macmaneslab/al2025/isoform/STAR_mappings/blu7-x_female_gonad_stress_STAR_anno_Aligned.sortedByCoord.out.bam \ > --Control:control /mnt/lustre/macmaneslab/al2025/isoform/STAR_mappings/L-G107_male_gonad_control_STAR_anno_Aligned.sortedByCoord.out.bam...
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Zong Jie posted a comment on discussion General Discussion
We updated a file 'UserManual.pdf' accompanied with the program in the zip package....
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Yungang Xu posted a comment on discussion General Discussion
To the author of the CASH. Could you please provide a document to descript the output...
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