How to fetch assembled sequences of different libraries from BAM

Question

[aditigrawal]

Hi All, I have 4 RNA-seq libraries ( control and treated in replicates). I merge them together to assemble them. Now, after assembly, I have got only single fasta file. How can I fetch sequences of individual libraries. Thanks Aditi Agrawal

[finswimmer]

Hallo aditigrawal,

some questions about this:

• fasta or fastq?
• Why have you merge the data if you than want to fetch sequences of individual libraries?
• Please show us some example headers of the sequences. Because this is the only where how one can differ the libraries.

fin swimmer

[Nitin Narwade]

If you have generated Denovo assembly one possible way could be, map raw reads individually on merged assembly using aligner like abowtie, bowtie2 etc. It will result in the individual alignment file (.sam; subsequently you can convert it into .bam using samtools view utility). Then you can simply find out read count (i.e. the number of raw reads supported to a particular transcript) using samtools idxstat. As your mapping each sample separately you will get separate read count. Then you can use the transcript ids obtained in read count table you can get sequences for individual samples using some programs like faSomeRecord developed under UCSC toolkit.

By the way why you want sequences for each sample separately?