I have used ballgown on 150 samples. And the ballgown outputs are like below:
Sample1
|_____ e2t.ctab
|_____ e_data.ctab
|_____ Sample1.gtf
|_____ i2t.ctab
|_____ i_data.ctab
|_____ t_data.ctab
Sample1.gtf looks:
# stringtie -e -B -p 8 -G /path/stringtie_output/stringtie_merged.gtf -o /path/Sample1.gtf /path/Sample1.sorted.bam
# StringTie version 1.3.3
chr1 StringTie transcript 10001 10390 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.1"; cov "0.0"; FPKM "0.000000"; TPM "0.000000";
chr1 StringTie exon 10001 10101 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.1"; exon_number "1"; cov "0.0";
chr1 StringTie exon 10179 10390 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.1"; exon_number "2"; cov "0.0";
chr1 StringTie transcript 10001 10465 . - . gene_id "MSTRG.6918"; transcript_id "MSTRG.6918.2"; cov "0.0"; FPKM "0.000000"; TPM "0.000000";
chr1 StringTie exon 10001 10167 . - . gene_id "MSTRG.6918"; transcript_id "MSTRG.6918.2"; exon_number "1"; cov "0.0";
chr1 StringTie exon 10423 10465 . - . gene_id "MSTRG.6918"; transcript_id "MSTRG.6918.2"; exon_number "2"; cov "0.0";
chr1 StringTie transcript 10001 10467 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.2"; cov "0.0"; FPKM "0.000000"; TPM "0.000000";
chr1 StringTie exon 10001 10101 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.2"; exon_number "1"; cov "0.0";
chr1 StringTie exon 10173 10249 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.2"; exon_number "2"; cov "0.0";
chr1 StringTie exon 10398 10467 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.2"; exon_number "3"; cov "0.0";
chr1 StringTie transcript 10001 10467 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.3"; cov "0.0"; FPKM "0.000000"; TPM "0.000000";
chr1 StringTie exon 10001 10101 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.3"; exon_number "1"; cov "0.0";
chr1 StringTie exon 10173 10224 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.3"; exon_number "2"; cov "0.0";
chr1 StringTie exon 10391 10467 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.3"; exon_number "3"; cov "0.0";
chr1 StringTie transcript 10005 10467 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.4"; cov "0.0"; FPKM "0.000000"; TPM "0.000000";
chr1 StringTie exon 10005 10178 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.4"; exon_number "1"; cov "0.0";
chr1 StringTie exon 10361 10467 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.4"; exon_number "2"; cov "0.0";
chr1 StringTie transcript 10011 10467 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.5"; cov "0.0"; FPKM "0.000000"; TPM "0.000000";
chr1 StringTie exon 10011 10178 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.5"; exon_number "1"; cov "0.0";
chr1 StringTie exon 10405 10467 . + . gene_id "MSTRG.6917"; transcript_id "MSTRG.6917.5"; exon_number "2"; cov "0.0";
chr1 StringTie transcript 10001 10465 1000 - . gene_id "MSTRG.6918"; transcript_id "MSTRG.6918.1"; cov "0.567742"; FPKM "0.066922"; TPM "0.283503";
chr1 StringTie exon 10001 10465 1000 - . gene_id "MSTRG.6918"; transcript_id "MSTRG.6918.1"; exon_number "1"; cov "0.567742";
chr1 StringTie transcript 11612 14409 . + . gene_id "MSTRG.7557"; transcript_id "MSTRG.7557.1"; cov "0.0"; FPKM "0.000000"; TPM "0.000000";
chr1 StringTie exon 11612 12697 . + . gene_id "MSTRG.7557"; transcript_id "MSTRG.7557.1"; exon_number "1"; cov "0.0";
chr1 StringTie exon 12975 13052 . + . gene_id "MSTRG.7557"; transcript_id "MSTRG.7557.1"; exon_number "2"; cov "0.0";
chr1 StringTie exon 13221 14409 . + . gene_id "MSTRG.7557"; transcript_id "MSTRG.7557.1"; exon_number "3"; cov "0.0";
I actually want the transcript_id and TPM as two columns for each sample of my 150 sample gtfs. How do I do that with awk or any other way to export the two columns from all files into a single file.
For each of the 150 files, assign an awk variable with the filename without the .gtf extension. Use ; as a delimiter and where the first column matches "trascript", print 3 columns, the first being the sample id variable you assigned above, the second being the transcript_id field and the third being the TPM field. Append output across all files to a single combined output file.
You should be able to write your awk command using the above logic.
this is what I don't know how to do. Can you please help me with an example. thanq
I actually tried the below command for one of the file
grep -P "\ttranscript\t" sample.gtf | cut -f9 | awk '{gsub("\"","",$0);gsub(";","",$0);print $4,$12}'
And this gave an output like below:
MSTRG.7557.1
ENST00000456328.2 0.000000
ENST00000450305.2 0.000000
MSTRG.7557.4
MSTRG.7558.1
MSTRG.7558.3
MSTRG.7558.4
MSTRG.7558.10
MSTRG.7558.14
MSTRG.7558.15
MSTRG.7558.18
MSTRG.7558.23
Explore awk online. You'll need the awk -v option. And always use the -F option to specify IFS - better safe than sorry.
If you use cut first and pipe the output to awk, you'll need to use something like a shell variable to get the sample name from the filename. You need neither grep nor awk. awk can operate on lines that match a pattern, like so: $1 ~ /transcript/ { do_something; }
for f in *.gtf
do
awk -v SMPL_NAME=$(basename $f} -F ";" ' .... ' $f >>overall_output.txt
done
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