Hi all,
I have questions regarding the strand info after TopHat and Cufflinks in NON-strand-specific experiments. I tried to look for the answers in the forum and in the web – but did not manage, so I am posting it here.
I have Illumina RNA seq reads, from a library that was prepared with NON-strand specific protocol.
1. I saw in tophat manual that TopHat will treat reads as strand specific. What option should I use when running TopHat if my reads are not strand specific?
2. After TopHat – in the bam files – Will I get strand for all reads? Or only for junction read?
In the bam file – will I have a strand according to the splice junction orientation or according the actual strand the read was mapped to?
3. Cufflinks gives “a guess” to the strand of the transcript. How is this guess made?
Thanks a lot.
I have questions regarding the strand info after TopHat and Cufflinks in NON-strand-specific experiments. I tried to look for the answers in the forum and in the web – but did not manage, so I am posting it here.
I have Illumina RNA seq reads, from a library that was prepared with NON-strand specific protocol.
1. I saw in tophat manual that TopHat will treat reads as strand specific. What option should I use when running TopHat if my reads are not strand specific?
2. After TopHat – in the bam files – Will I get strand for all reads? Or only for junction read?
In the bam file – will I have a strand according to the splice junction orientation or according the actual strand the read was mapped to?
3. Cufflinks gives “a guess” to the strand of the transcript. How is this guess made?
Thanks a lot.
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