Hi there,
I have a question about reads coverage and RNA-seq. I am analyzing our Illumina paired-end data that we obtained from bacterial mRNA with Artemis (alignement with BWA) and I noticed some "funny" coverage profiles. With all the experts on this forum, I am sure one of you will be able to help me.
case #1
On this picture we can see that gene B is expressed a lot compared to others. Also, we can see that the signal obtained from gene B's mRNA seems to "decay" on the beginning of gene A and the inter-ORF. How can this phenomenon can be explained ?
case #2
Notice the big bump upstream of gene B. It looks like some unreliable annotation or some cryptic-mRNA, what do you think ?
Is there any software / pipeline that takes into account case #1 and also discover/correct known genome annotations ?
Thank you for your comments and answers,
pasta
I have a question about reads coverage and RNA-seq. I am analyzing our Illumina paired-end data that we obtained from bacterial mRNA with Artemis (alignement with BWA) and I noticed some "funny" coverage profiles. With all the experts on this forum, I am sure one of you will be able to help me.
case #1
On this picture we can see that gene B is expressed a lot compared to others. Also, we can see that the signal obtained from gene B's mRNA seems to "decay" on the beginning of gene A and the inter-ORF. How can this phenomenon can be explained ?
case #2
Notice the big bump upstream of gene B. It looks like some unreliable annotation or some cryptic-mRNA, what do you think ?
Is there any software / pipeline that takes into account case #1 and also discover/correct known genome annotations ?
Thank you for your comments and answers,
pasta
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