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Is featureCounts suitable for lncRNA quantification? #2

Open qingzengLi opened 1 week ago

qingzengLi commented 1 week ago

I'm trying to use featureCounts to quantify lncRNA data, the lncRNA gtf file is generated from stringtie. I find that the expression matrix is different from the matrix generated by stringtie.Which software is more accurate? Here are the commads

stringtie -e -G lncRNA.gtf -p 8 -A ${id}_abundance.txt -o s${id}.gtf 03.align/*.bam
python prepDE.py -i sample-gtf.txt -g lncRNA-count.csv -t lncRNA-transcript-count.csv

featureCounts -T 20 -p -B -C -f -t transcript -g transcript_id -o all_features.txt -a lncRNA.gtf 03.align/*.bam
qingzengLi commented 1 week ago

In addition, the quantification of mRNA showed a high correlation

ShiLab-Bioinformatics commented 6 days ago

Different tools can give different results because of the differences between algorithms and settings. Can you provide more details about how the results are different?

qingzengLi commented 6 days ago

Sure,thanks for your reply,my gtf file like this

1       StringTie       transcript      15355   19694   1000    +       .       gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; 
1       StringTie       exon    15355   15514   1000    +       .       gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; 
1       StringTie       exon    16251   16436   1000    +       .       gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "2"; 
1       StringTie       exon    17155   19694   1000    +       .       gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "3"; 
1       StringTie       transcript      15768   19694   1000    +       .       gene_id "MSTRG.1"; transcript_id "MSTRG.1.2"; 
1       StringTie       exon    15768   15973   1000    +       .       gene_id "MSTRG.1"; transcript_id "MSTRG.1.2"; exon_number "1"; 
1       StringTie       exon    16152   16533   1000    +       .       gene_id "MSTRG.1"; transcript_id "MSTRG.1.2"; exon_number "2"; 
1       StringTie       exon    16713   18090   1000    +       .       gene_id "MSTRG.1"; transcript_id "MSTRG.1.2"; exon_number "3"; 
1       StringTie       exon    18271   19694   1000    +       .       gene_id "MSTRG.1"; transcript_id "MSTRG.1.2"; exon_number "4"; 
1       StringTie       transcript      15768   19694   1000    +       .       gene_id "MSTRG.1"; transcript_id "MSTRG.1.3"; 
1       StringTie       exon    15768   15973   1000    +       .       gene_id "MSTRG.1"; transcript_id "MSTRG.1.3"; exon_number "1"; 
1       StringTie       exon    16152   16331   1000    +       .       gene_id "MSTRG.1"; transcript_id "MSTRG.1.3"; exon_number "2"; 
1       StringTie       exon    17791   19694   1000    +       .       gene_id "MSTRG.1"; transcript_id "MSTRG.1.3"; exon_number "3";

And I checked the values of the same lncRNAs in the same samples using two different quantification methods, and found that the values in the two matrices show no correlation image