I can't recreate this. When I try --no-discordant, XS:i flags still appear as expected. Can you supply a small example where an XS:i is suppressed spuriously?
Best,
Ben
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I can easily reproduce this and I just verified that the problem persists in beta7. Below are a few lines from my logs showing the params used. Shall I email you the fastq files (about 800K each gzipped) of 10K reads? The target is the standard hg19.
When run with --no-discordant there are no XS:i records.
When run without --nodiscordant, there are 5903 XS:i records.
/Sol.
LOG WITH --no-discordant
running bowtie with options: --phred33 --minins 0 --maxins 700 --fr --end-to-end --sensitive --no-mixed --no-discordant --no-dovetail --no-contain -M 5 -p 4
running bowtie from index directory: /hive/groups/wet/illumina/bowtie2_genomes/hg19/
running bowtie on ebwt model: hg19
applying bowtie option for SAM output format
using bowtie options that SAVE reads that are unreported in bowtie output files
/cluster/home/sol/mycvs/kent/src/hg/bowtie2/bowtie2/bowtie2 -x hg19 -q -t -1 /scratch/sol-15962-1343411200/input.hEBw1_fj101_00of30_10K_1.fastq -2 /scratch/sol-15962-1343411200/input.hEBw1_fj101_00of30_10K_2.fastq --phred33 --minins 0 --maxins 700 --fr --end-to-end --sensitive --no-mixed --no-discordant --no-dovetail --no-contain -M 5 -p 4 --un-conc /scratch/sol-15962-1343411200/hEBw1_fj101_00of30_10K_filtered_beta7_unmapped_%.fastq -S /scratch/sol-15962-1343411200/temp.hEBw1_fj101_00of30_10K_filtered_beta7_hg19bowtie.sam
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
Time loading reference: 00:00:52
Time loading forward index: 00:04:21
Time loading mirror index: 00:03:04
Multiseed full-index search: 00:00:03
10000 reads; of these:
10000 (100.00%) were paired; of these:
1131 (11.31%) aligned concordantly 0 times
5911 (59.11%) aligned concordantly exactly 1 time
2958 (29.58%) aligned concordantly >1 times
88.69% overall alignment rate
-----------------------------------
LOG WITHOUT --no-discordant
running bowtie with options: --phred33 --minins 0 --maxins 700 --fr --end-to-end --sensitive --no-mixed --no-dovetail --no-contain -M 5 -p 4
running bowtie from index directory: /hive/groups/wet/illumina/bowtie2_genomes/hg19/
running bowtie on ebwt model: hg19
applying bowtie option for SAM output format
using bowtie options that SAVE reads that are unreported in bowtie output files
/cluster/home/sol/mycvs/kent/src/hg/bowtie2/bowtie2/bowtie2 -x hg19 -q -t -1 /scratch/sol-15876-1343411158/input.hEBw1_fj101_00of30_10K_1.fastq -2 /scratch/sol-15876-1343411158/input.hEBw1_fj101_00of30_10K_2.fastq --phred33 --minins 0 --maxins 700 --fr --end-to-end --sensitive --no-mixed --no-dovetail --no-contain -M 5 -p 4 --un-conc /scratch/sol-15876-1343411158/hEBw1_fj101_00of30_10K_filtered_beta7_unmapped_%.fastq -S /scratch/sol-15876-1343411158/temp.hEBw1_fj101_00of30_10K_filtered_beta7_hg19bowtie.sam
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
Time loading reference: 00:01:32
Time loading forward index: 00:04:21
Time loading mirror index: 00:03:04
Multiseed full-index search: 00:00:03
10000 reads; of these:
10000 (100.00%) were paired; of these:
1131 (11.31%) aligned concordantly 0 times
5911 (59.11%) aligned concordantly exactly 1 time
2958 (29.58%) aligned concordantly >1 times
----
1131 pairs aligned concordantly 0 times; of these:
4 (0.35%) aligned discordantly 1 time
88.73% overall alignment rate
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Can you try again with Bowtie 2 2.0.3? I fixed a problem in that version with an interaction between --no-discordant and --no-mixed. I bet it fixes this problem.
Best,
Ben
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I can't recreate this. When I try --no-discordant, XS:i flags still appear as expected. Can you supply a small example where an XS:i is suppressed spuriously?
Best,
Ben
I can easily reproduce this and I just verified that the problem persists in beta7. Below are a few lines from my logs showing the params used. Shall I email you the fastq files (about 800K each gzipped) of 10K reads? The target is the standard hg19.
When run with --no-discordant there are no XS:i records.
When run without --nodiscordant, there are 5903 XS:i records.
/Sol.
LOG WITH --no-discordant
running bowtie with options: --phred33 --minins 0 --maxins 700 --fr --end-to-end --sensitive --no-mixed --no-discordant --no-dovetail --no-contain -M 5 -p 4
running bowtie from index directory: /hive/groups/wet/illumina/bowtie2_genomes/hg19/
running bowtie on ebwt model: hg19
applying bowtie option for SAM output format
using bowtie options that SAVE reads that are unreported in bowtie output files
/cluster/home/sol/mycvs/kent/src/hg/bowtie2/bowtie2/bowtie2 -x hg19 -q -t -1 /scratch/sol-15962-1343411200/input.hEBw1_fj101_00of30_10K_1.fastq -2 /scratch/sol-15962-1343411200/input.hEBw1_fj101_00of30_10K_2.fastq --phred33 --minins 0 --maxins 700 --fr --end-to-end --sensitive --no-mixed --no-discordant --no-dovetail --no-contain -M 5 -p 4 --un-conc /scratch/sol-15962-1343411200/hEBw1_fj101_00of30_10K_filtered_beta7_unmapped_%.fastq -S /scratch/sol-15962-1343411200/temp.hEBw1_fj101_00of30_10K_filtered_beta7_hg19bowtie.sam
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
Time loading reference: 00:00:52
Time loading forward index: 00:04:21
Time loading mirror index: 00:03:04
Multiseed full-index search: 00:00:03
10000 reads; of these:
10000 (100.00%) were paired; of these:
1131 (11.31%) aligned concordantly 0 times
5911 (59.11%) aligned concordantly exactly 1 time
2958 (29.58%) aligned concordantly >1 times
88.69% overall alignment rate
-----------------------------------
LOG WITHOUT --no-discordant
running bowtie with options: --phred33 --minins 0 --maxins 700 --fr --end-to-end --sensitive --no-mixed --no-dovetail --no-contain -M 5 -p 4
running bowtie from index directory: /hive/groups/wet/illumina/bowtie2_genomes/hg19/
running bowtie on ebwt model: hg19
applying bowtie option for SAM output format
using bowtie options that SAVE reads that are unreported in bowtie output files
/cluster/home/sol/mycvs/kent/src/hg/bowtie2/bowtie2/bowtie2 -x hg19 -q -t -1 /scratch/sol-15876-1343411158/input.hEBw1_fj101_00of30_10K_1.fastq -2 /scratch/sol-15876-1343411158/input.hEBw1_fj101_00of30_10K_2.fastq --phred33 --minins 0 --maxins 700 --fr --end-to-end --sensitive --no-mixed --no-dovetail --no-contain -M 5 -p 4 --un-conc /scratch/sol-15876-1343411158/hEBw1_fj101_00of30_10K_filtered_beta7_unmapped_%.fastq -S /scratch/sol-15876-1343411158/temp.hEBw1_fj101_00of30_10K_filtered_beta7_hg19bowtie.sam
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
Time loading reference: 00:01:32
Time loading forward index: 00:04:21
Time loading mirror index: 00:03:04
Multiseed full-index search: 00:00:03
10000 reads; of these:
10000 (100.00%) were paired; of these:
1131 (11.31%) aligned concordantly 0 times
5911 (59.11%) aligned concordantly exactly 1 time
2958 (29.58%) aligned concordantly >1 times
----
1131 pairs aligned concordantly 0 times; of these:
4 (0.35%) aligned discordantly 1 time
88.73% overall alignment rate
Can you try again with Bowtie 2 2.0.3? I fixed a problem in that version with an interaction between --no-discordant and --no-mixed. I bet it fixes this problem.
Best,
Ben