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reads mapping

reads mapping# Biology - 生物学

G*G2014-04-29 07:04

1 楼

I mapped a read into a gene.
The read falls into the range of starting and ending of the gene.
But the strand of the read is negative and the gene's strand is positive.
Can we say the read belongs to the gene?
How to annotate the read?

l*e2014-04-29 07:04

2 楼

No. It's a novel transcript.

G*G2014-04-29 07:04

3 楼

thanks. I have another question about next generation sequencing.
suppose you get a lot of reads from RNA-seq.
and you have a reference genome where Chr1 is positive strand.
when bowtie aligns reads into the reference Chr1,
will it consider the alignment in positive strand
and in negative strand?

【在 l********e 的大作中提到】

: No. It's a novel transcript.

l*e2014-04-29 07:04

4 楼

Depends on your settings.
Under standard setting, bowtie will try to align both strands.
I'm not a professional bioinformatician though .. better double check this.

【在 G***G 的大作中提到】

: thanks. I have another question about next generation sequencing.
: suppose you get a lot of reads from RNA-seq.
: and you have a reference genome where Chr1 is positive strand.
: when bowtie aligns reads into the reference Chr1,
: will it consider the alignment in positive strand
: and in negative strand?

G*G2014-04-29 07:04

5 楼

thanks.

【在 l********e 的大作中提到】

: Depends on your settings.
: Under standard setting, bowtie will try to align both strands.
: I'm not a professional bioinformatician though .. better double check this.

h*t2014-04-29 07:04

6 楼

you may check bowtie's option: --nofw/--norc
http://bowtie-bio.sourceforge.net/manual.shtml#alignment

x*e2014-04-29 07:04

7 楼

因为在你准备library的时候已经丢失了strand的信息（通常的protocol），结果是一
半的reads会map到positive，一半会map到negative，
还是你发现的那个read，很有可能是mapping错误，除非你发现很多reads，都如此
mapping，即使这样，也要考虑有没有可能是repeat导致的

g*62014-04-29 07:04

8 楼

yes。这取决于你RNA-seq建库用的试剂盒是不是directional的。directional试剂盒的
确只能测到正义链,non-directional的正反义都也可测到。二楼是错的。

【在 x*********e 的大作中提到】

: 因为在你准备library的时候已经丢失了strand的信息（通常的protocol），结果是一
: 半的reads会map到positive，一半会map到negative，
: 还是你发现的那个read，很有可能是mapping错误，除非你发现很多reads，都如此
: mapping，即使这样，也要考虑有没有可能是repeat导致的