Are those total RNA (Transcriptome) sequencing samples? If so,
1) FastQC (Check quality of sequencing).
2) Trimmomatic or Cutadapt (if necessary, uncleaned reads for adapters)
3) STAR or HISAT2 (I would personally recommend STAR)
4) SAMstat (Check quality of alignment)
5) featureCount (Check mapping quality, MAPQ using SAMstat from alignment before starting quantification)
6) DESeq2 or edgeR (Differential expression analysis)
7) GeneSCF v1.1 (command-line)/Enrichr (Web-based) [Gene ontology or pathway analysis for differentially expressed genes, this step is only applicable for protein coding genes]
If you are specifically looking for/analyzing long noncoding RNAs, use annotation from Gencode lncRNAs in step 3 (alignment/assembly) and step 5 (Gene/Transcript quantification)
ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.long_noncoding_RNAs.gtf.gz (HG19 genome)
You can also use the updated version, if you are going to use HG38 genome in step 3
Have a look at this post describing on how to ask questions: How To Ask Good Questions On Technical And Scientific Forums
For a problem like this I would advice you to always first look up some papers from similar research and have a look at their pipeline.
you may also like to visit the ENCODE pipeline https://www.encodeproject.org/rna-seq/long-rnas/