Reference Genome Sequence file Ref.fa

Question

[Mian Numan]

as far i know because i am learning Bioinformatics so the -----.fq A FASTQ file has four line-separated fields per sequence. but when i open .fq file with then it showed the chr22 after that only NNNNNNNNNNNNNNNN

what is the problem please help me

[seidel]

You're right in that fastq files have 4 lines per sequence record. However, the fastq file would not show chr22, because the fastq file has no alignment information (it doesn't record the origin or match of a sequence). (1) Do you mean to say that you sequenced chr22, so the file should contain sequence matching chr22 but all you saw were NNNNs? Can you clarify? (2) If you see N's in a fastq file, it means the sequencer could not determine the base call for that sequence position. Can you paste the frist 4 or 8 lines of your fastq?

[Mian Numan]

Sir, I got this data from my friend, and he advised me to use this data for practice.

Yes this is the sequence fie for chromosome no 22 (don’t know which organism)

The sequence of .fq file are here

>chr22
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

But When I open the .gtf file then it shows this

chr22   ENSEMBL gene    10736171    10736283 

[GenoMax]

This sequence is plain fasta format sequence for chr22. This is not a fastq format sequence. N are generally padded to these sequences to indicate the fact that not every base present in chromosomes is sequenceable (e.g. telomeres, centromeres) but a sequence exists at that location.

[Mian Numan]

Thank you sir

[Mian Numan]

sir actually I am learning the

Bioinformatics Approaches to Studying Plant Long Noncoding RNAs (lncRNAs): Identification and Functional Interpretation of lncRNAs from RNA-Seq Data Sets