I need to get the raw read counts of a *pseudomonas aeruginosa UCBPP-PA14 * RNASeq data set.
After mapping with "Bowtie for Illumina", I run HTSeq-counts using 2 version of pseudomonas aeruginosa UCBPP-PA14 gft files obtained from ensembl and pseudomonas genome databases, however htseq-counts resulted in to empty file telling that no reads could be mapped.
Similarly I tried featureCounts , but again it could not map any read.
Have you had a look at your .bam file in IGV? This will allow you to visualise the alignments from Bowtie and indicate if the problem lies at your mapping stage.
where the columns correspond to the names of the chromosome, their length, the number of mapped reads and the number of unmapped reads.
Make sure that a) you have mapped reads and b) that the chromosome names are exactly the same as those in the first column of the GTF file that you use with featureCounts/HTSeqCounts.
Have you had a look at your .bam file in IGV? This will allow you to visualise the alignments from Bowtie and indicate if the problem lies at your mapping stage.