Hello.

I used a ncRNA.fa to alignment using RNA-seq samples in TOPHAT

*FASTA:

>ENSSSCT00000024762.1 ncrna:novel chromosome:Sscrofa10.2:2:114672074:114672179:1 gene:ENSSSCG00000023111.1 gene_biotype:snRNA transcript_biotype:snRNA gene_symbol:U6 description:U6 spliceosomal RNA [Source:RFAM;Acc:RF00026]
GCGTCACTGTAGTAGCACACAGACTAAAACTGGAATGATACAGAGAAGATTAGCATAGAT
ACTGTGCCAGAATGGTGTATAAATTAAGGAAGCATTCTGTATTTTT*

My bam file its ok. There are sequence mapped. I look in igv the counts.

*HWI-7001432L:169:C7A9GANXX:2:1101:1151:88174    83      ENSSSCT00000019656.3    166     50      76M     =       80      -162    GAAACAGCAGTGATAAAAATTAAGCCATGAACGAAAGTTTGACTAAGTTATATTAATTAGAGTTGGTAAATCTCGT   1GGGGGGGGEGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGFF1GGGGGGGGGGGGGGBBB@A  AS:i:0   XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:76 YT:Z:UU NH:i:1*

Im using a GTF from ensembl (that include no-coding genes)

   * x havana  exon    112829213       112829236       .       +       .       exon_id "ENSSSCE00000248122"; exon_number "2"; exon_version "1"; gene_biotype "lincRNA"; gene_id "ENSSSCG00000030972"; gene_name "CH242-64G23.3"; gene_source "havana"; gene_version "1"; havana_transcript "OTTSUST00000012069"; havana_transcript_version "1"; transcript_biotype "lincRNA"; transcript_id "ENSSSCT00000033495"; transcript_name "CH242-64G23.3-001"; transcript_source "havana"; transcript_version "1"; tss_id "TSS25916";*

However, when I tried to calculted the counts by ht-seq... all transcripts appear 0 counts. I tried to change default parametres... but I did not succeed

Can anybody help me?

Thanks a lot!!