Simon Heath

Dear Bekir, Apologies for the delay and I will get back to this issue now. Simon > On 13 Sep 2018, at 13:43, berguner wrote: > > Dear Simon, >...

Dear Bekir, I can't reproduce the problem. When I map the sample file you sent, I see many reads that start with CG and almost all of them are mapping...

Not sure when this changed, but the version on git does not show this problem. Here is the BAM for these reads, and all of them give full length alignments....

In my last reply I sent the BAM I generated for the reads you sent me. No special parameters were used. This is very odd! Simon > On 9 Oct...

Maybe attachments are removed when sent through github. I’ll send it to you directly. Simon > On 9 Oct 2018, at 17:51, berguner wrote: > > Sorry but I could...

Could you send me an email address I can use to sned you the BAM file? Simon > On 9 Oct 2018, at 17:51, berguner wrote: > > Sorry but...

Bod orientation are read pairs that are not 'standard' Illumina pair-ends (i.e, both pairs on different strands of the same contig with the read on the + strand being before...

Could there be a problem with disk space that’s leading to the failures? > On 27 Aug 2018, at 12:42, Ismail Moghul wrote: > > The above errors disappeared when...

Does the contig ‘chr14-GL’ exist in the reference? > On 27 Aug 2018, at 12:47, Ismail Moghul wrote: > > That was the first thing I checked - there was...

And the chr14_GL0000*_random contigs do exist in the reference given to the caller? > On 27 Aug 2018, at 12:53, Ismail Moghul wrote: > > No, but it doesn't exist...