#BASH GREP UNIQUE LINES FROM A FILE HOW TO#

How many lines do you see now? Click here to check your output $ cut -f 1,4 chr1-hg19_genes.gtf | sort -u | wc -l In a GTF file, this exon will be represented multiple times, once for each transcript (or splice isoform).

Given our understanding of splice isoforms, we know that a given exon can be part of 2 or more different transcripts generated from the same gene. The columns in the GTF file contain the genomic coordinates (location) of gene features (exon, start_codon, stop_codon, CDS) along with the associated gene_names, transcript_ids and protein_ids (p_id). That information is specifically about all the various entities or features found in a genome in this case, on chromosome 1.įor more information on this file format, check out the Ensembl site. The GTF (Gene Transfer Format) file is a tab-delimited file with information arranged in a very specific manner, usually for NGS analysis. In order to demonstrate this let’s first view a smaller file that you have.Ĭhr1 unknown exon 14362 14829. This will return everything that does not match the pattern. One last grep option you might find quite useful is the -v option, which does an inverted match. Using the argument -no-group-separator with grep will disable this small thing you should note is that when using the -n option, lines that have a : after the line number correspond to the lines with the match (e.g 861214:CACTTGTAAGGGCAGGCCCCCTTCACCCTCCCGCTCCTGGGGGANNNNNNNNNNANNN.), while lines with a - after the line number are the surrounding lines retrieved when using the -A and/or -B options (e.g. This might be problematic if you are trying to maintain the FASTQ file structure or if you simply do not want them in your output. You will notice that when we use the -B and/or -A arguments with the grep command, the output has some additional lines with dashes ( -), these dashes work to separate your returned “groups” of lines and are referred to as “group separators”.

#BASH GREP UNIQUE LINES FROM A FILE HOW TO#

More about searching text files with grep Group separators ( -), and how to remove them The output returns 5 sequences for Mov10_oe_1 and 3 sequences for Mov10_oe_2. Grep -B 1 CTCAATGAGCCA Mov10_oe_1.subset.fq If you want to search for that sequence in all Mov10 replicate fastq files, what command would you use? Answers In addition to finding the sequence, how can you modify the command so that your search also returns the name of the sequence? A whole FASTQ record for a single read should appear similar to the for the sequence CTCAATGAGCCA in Mov10_oe_1.subset.fq. Each sequencing read in a FASTQ file is associated with four lines, with the first line (header line) always starting with an symbol. Let’s give it a try by searching the FASTQ files in the raw_fastq directory.įASTQ files contain the sequencing reads (nucleotide sequences) output from a sequencing facility. The pattern that we want to search is specified in search_term slot, and the file we want to search within is specified in the filename slot. The syntax for grep is as follows: grep search_term filename. Why the word “grep”? It is a shortened form of globally search for a regular expression and print matching lines (g/re/p). Simply put grep is a command-line utility for searching plain-text data sets for lines matching a pattern or regular expression (regex). We can also search within files without even opening them, using grep.

We went over how to search within a file using less. Use the pipe ( |) character to chain together commands.Write to and append a file using output redirection.Search for characters or patterns in a text file using the grep command.The Shell: Searching and Redirection View on GitHubĪpproximate time: 60 minutes Learning objectives The Shell: Searching and Redirection | Introduction to the command line interface (Shell) Skip to the content.

Bash grep unique lines from a file