I'm new in NGS data analysis. Recently, we sequenced a hairpin library (~1000 shRNA) for quality and We already got the fastq file from illumna. We need to get information from this fastq file: How many reads for each of the shRNA in library.
Please suggest is it possible for me to do it by myself? The fastq file is so big, my PC can not read it.
Thanks in advance.
You would need to use a dedicated high performance cluster to read the FASTQ files. Furthermore, you need command line tools for reading these files. In order to simply test how many reads are there in FASTQ file you can use FASTQC, but these are linux command line tools and dont easily work on other operating systems.
When someone talks about NGS analysis and MS office, it is pretty obvious that the person lacks some basic understanding of NGS data processing. In this case I would highly recommend to get help with someone with more experience/understanding or get the basics of data processing before doing anything with the data. Doing anything without proper planning and knowledge will only waste time.
After Quality control, Mapping to shRNA sequences, you can use software such as SAMtools or HTSeq to count the number of reads mapped to each shRNA sequence. These tools can generate read counts for each shRNA in a tabular format.
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