The left reads map 95% while the right reads map only 0.7% using tophat

[s_halawa]

I have a problem. I try aligning paired end data of restrictive heart cardiomyopathy using tophat and I get this summary:
tophat2 -o trialtophatRestrictive3 -p 20 -G /data2/hg19/genes.gtf /data2/hg19/genome SRR2138385_1.fastq SRR2138385_2.fastq
Left reads:
Input : 56776839
Mapped : 54092930 (95.3% of input)
of these: 3069097 ( 5.7%) have multiple alignments (4267 have >20)
Right reads:
Input : 56776839
Mapped : 420422 ( 0.7% of input)
of these: 21837 ( 5.2%) have multiple alignments (32 have >20)
48.0% overall read mapping rate.

Aligned pairs: 411231
of these: 21368 ( 5.2%) have multiple alignments
8215 ( 2.0%) are discordant alignments

The left reads map 95% while the right reads map only 0.7%
What should I do?
I did fastqc before tophat and the reports for the forward and reverse were fine.
I appreciate your help
Thanks alot
Sarah

[kmcarr]

Cross posted on BioStar

https://www.biostars.org/p/171389/

as well as in General and Bioinformatics forum here

http://seqanswers.com/forums/showthread.php?t=65297

http://seqanswers.com/forums/showthread.php?t=65300

[s_halawa]

Hey kmcarr,
All these links are posts made by me I'm kind of desperate to solve this problem.
Thanks,
Sarah

[westerman]

I'm kind of desperate to solve this problem.

Obviously.

kmcarr is pointing out that is not polite to cross-post the same message/question to multiple forums within the same bulletin board. By doing so you end up with different people answering the question in different threads thus causing a lot of confusion and a duplication of effort which wastes everyone's time.

kmcarr is also pointing out that to some people it is also not polite to post the same message to multiple related bulletin boards -- e.g., biostars and SeqAnswers -- for the same reasons as above: you will waste the time of people who read both bulletin boards and have to mentally merge the replies from both.

I see that Biostars (which I do not read on a regular basis) has given you some replies. I'll see if I come up with something useful to comment on.

[westerman]

Antonio from Biostars has the best suggestion. Map only the supposedly poor-mapping R2 reads (SRR2138385_2.fastq). See if you get the same results as when you map R1 and R2 together. If

(a) if you get the same results then your R2 reads are not from human; figure out where they come from?

(b) if you get radically different results (i.e., by themselves the R2 reads map at 90+%) then there is a problems with R1+R2. Most like that the reads are out of order.

[s_halawa]

I am very sorry! I'm really new to the notions of forums. But I understand your point and I'm hinestly and truly very sorry. I will erase the posts from the different groups, and leave it only in one thread. Thank you for pointing this out to me and thank you also very much for your advice and help.

[s_halawa]

I am very sorry kmcarr fir this honest mistake. I'm really new to this idea of forums, this was my first post ever, but now I understand. I want to erase all posts and leave just one thread. Can you tell me how to delete posts on forums, I can't find any delete feature. Thank you

[GenoMax]

I am very sorry kmcarr fir this honest mistake. I'm really new to this idea of forums, this was my first post ever, but now I understand. I want to erase all posts and leave just one thread. Can you tell me how to delete posts on forums, I can't find any delete feature. Thank you

I have deleted the duplicate posts. Normally "Delete" your own post option is under "Edit" section of your post but it may not become available to new users until they successfully post a certain number of times (may be ~10).

[s_halawa]

How can I delete this entire thread? Thank you

[westerman]

@s_halawa: Not to derail you from correct bulletin board etiquette but getting back to the bioinformatics problem, have you done what Antonio and I have suggested?