ctb · November 23, 2021 04:11 · peterjc · May 28, 2013
diff --git a/gistfile1.txt b/gistfile1.txt
 Hi bwa users,

 The bwa-mem manuscript has been rejected. Interestingly, the first
 reviewer only raised a couple of minor concerns and then accepted the
 manuscript in the second round of the review. The second reviewer made
 quite a few mistakes on some basic concepts and was hostile from the
 beginning. The third reviewer gave fair and good review in the first
 round, all of which have been addressed, but he then tried hard to
 argue one particular mapper to be the best in accuracy that on the
 contrary is inferior to most others in my view. I admit that my
 responses were not appropriate, either, when I was in rage under the
 charge of being "scientifically dishonest" - because I did not show
 that particular mapper in the main figure given its absence of mapping
 quality.

 Anyway, this is the past and you cannot really tell if I am the biased
 one when myself is describing the review process. As to the
 manuscript, I do not have plan to submit it to another peer-reviewed
 journal before I get time from the problems that interest me more. The
 manuscript is fairly short and simple. It should not be hard for you
 to judge how bwa-mem is compared to those peer-reviewed mappers. If
 you decide to use bwa-mem, please cite:

 "Li H. (2013) Aligning sequence reads, clone sequences and assembly
 contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN]."

 I would greatly appreciate. In these years, I sometimes did not pay
 enough attention to users' requests and sometimes even lost patience
 in answering questions. I deeply apologize for these. Just remember:
 when I calm down, I am always grateful to every user, really.

 Thank you very much,

 Heng


 PS: I regard this review process as an isolated event. I don't mean to
 criticize the journal or the peer-review process in general with this
 example. As I said, I was not doing everything in the best way,
 either.
	Hi bwa users,

	The bwa-mem manuscript has been rejected. Interestingly, the first
	reviewer only raised a couple of minor concerns and then accepted the
	manuscript in the second round of the review. The second reviewer made
	quite a few mistakes on some basic concepts and was hostile from the
	beginning. The third reviewer gave fair and good review in the first
	round, all of which have been addressed, but he then tried hard to
	argue one particular mapper to be the best in accuracy that on the
	contrary is inferior to most others in my view. I admit that my
	responses were not appropriate, either, when I was in rage under the
	charge of being "scientifically dishonest" - because I did not show
	that particular mapper in the main figure given its absence of mapping
	quality.

	Anyway, this is the past and you cannot really tell if I am the biased
	one when myself is describing the review process. As to the
	manuscript, I do not have plan to submit it to another peer-reviewed
	journal before I get time from the problems that interest me more. The
	manuscript is fairly short and simple. It should not be hard for you
	to judge how bwa-mem is compared to those peer-reviewed mappers. If
	you decide to use bwa-mem, please cite:

	"Li H. (2013) Aligning sequence reads, clone sequences and assembly
	contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN]."

	I would greatly appreciate. In these years, I sometimes did not pay
	enough attention to users' requests and sometimes even lost patience
	in answering questions. I deeply apologize for these. Just remember:
	when I calm down, I am always grateful to every user, really.

	Thank you very much,

	Heng


	PS: I regard this review process as an isolated event. I don't mean to
	criticize the journal or the peer-review process in general with this
	example. As I said, I was not doing everything in the best way,
	either.