Fastqc Download Github
Maryalice Cutcher
ChIPseqSpikeInFree: a ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in is a novel ChIP-seq normalization method to effectively determine scaling factors for samples across various conditions and treatments, which does not rely on exogenous spike-in chromatin or peak detection to reveal global changes in histone modification occupancy. The installation details can be found on github.
In the interest of saving time during this short workshop we will only indicate how fastqc is run, and will then focus on interpretation of typical output. More detailed information about actually running fastqc are available elsewhere on the RADCamp site.
In this example, the input is four filenames (one filename for each of our .zip files).Each time the loop iterates, it will assign a file name to the variable filenameand run the unzip command.The first time through the loop,$filename is Arabidopsis_sample1_fastqc.zip.The interpreter runs the command unzip on Arabidopsis_sample1_fastqc.zip.For the second iteration, $filename becomesArabidopsis_sample2_fastqc.zip. This time, the shell runs unzip on Arabidopsis_sample2_fastqc.zip.It then repeats this process for the four other .zip files in our directory.
To view the Fastqc results, you may open the fastqc_report.html file ina web browser or the summary.txt file (located in the zipped outputarchive) on the command line. For assistance copying files to your localmachine, please see the Moving Data page.
In this example, the list is six filenames (one filename for each of our .zip files).Each time the loop iterates, it will assign a file name to the variable filenameand run the unzip command.The first time through the loop,$filename is SRR097977_fastqc.zip. The interpreter runs the command unzip on SRR097977_fastqc.zip.For the second iteration, $filename becomes SRR098026_fastqc.zip. This time, the shell runs unzip on SRR098026_fastqc.zip.It then repeats this process for the four other .zip files in our directory.