Sequencing of cap RNA (5'-end) of C. elebans transcripts. Samples marked as 'short' refer to nascent transcrips before they are transpliced. The scientist isolated short (20-100nt) nuclear RNA with a 5' cap from embryos. 'Long' samples are capped RNA longher than 200nt that are already transpliced and can be used to validate the 'short' samples. Original sample GSM1050559 was discarded die to very poor mapping.
|1||GSM1050558_short_capRNA_1.sga||short cap RNA rep1||capRNA||GSM1050558|
|2||GSM1050560_short_capRNA_2.sga||short cap RNA rep2||capRNA||GSM1050560|
|3||GSM1050561_long_capRNA_1.sga||long cap RNA rep1||capRNA||GSM1050561|
|4||GSM1050562_long_capRNA_2.sga||long cap RNA rep2||capRNA||GSM1050562|
SRA files were downloaded from GEO GSE42819 and converted in FASTQ using fastq-dump program from sratoolkit. Files marked as 'long' were paired-end (used --split-3 flag). Mapping was done using Bowtie and sam files were converted in sga files using samtools and chipseq.