User: aleka

gravatar for aleka
aleka90
Reputation:
90
Status:
Trusted
Location:
United Kingdom
Last seen:
2 years, 2 months ago
Joined:
5 years, 3 months ago
Email:
a***********@gmail.com

about me

Posts by aleka

<prev • 38 results • page 1 of 4 • next >
0
votes
2
answers
1.5k
views
2
answers
Comment: C: fastqc and coverage
... yes I use the default parameters. that would make sense why CollectWgsMetrics gave a smaller coverage. ...
written 2.6 years ago by aleka90
0
votes
2
answers
1.5k
views
2
answers
Comment: C: fastqc and coverage
... good point about the uneven coverage. you reminded me to check. I didn't have though uneven coverage. more less the same. ...
written 2.6 years ago by aleka90
0
votes
2
answers
1.5k
views
2
answers
Comment: C: fastqc and coverage
... this was an answer to my initial question, if you didn't realise it. Aleka ...
written 2.6 years ago by aleka90
0
votes
2
answers
1.5k
views
2
answers
Answer: A: fastqc and coverage
... So I had calculated the duplicate rate according to fastqc, however this is not absolutely correct as it is an estimate of the first 100000seq. According to CollectWgsMetrics Tool and the metrics in MarkDuplicates, the duplicate rate is much higher, which fit the mean coverage, calculated with depth ...
written 2.6 years ago by aleka90
0
votes
2
answers
1.5k
views
2
answers
Comment: C: fastqc and coverage
... Hi all, Thanks for the feedback. The duplicate rate is based on fastqc that I run. After trimming and filtering, I don't have overrepresented seq or adapter content. The 50% duplication rate is after mapping, trimming. I loose a few million reads due to trimming but why doesn't explain the big los ...
written 2.6 years ago by aleka90
2
votes
2
answers
1.5k
views
2
answers
fastqc and coverage
... I have 50% duplicates on WGS on tumour samples and while I was expecting that the coverage will be reduced from 30x to 15x, it goes below 8x. So I am trying to figure out the reason that I have less coverage. I can see that I have a warning/failure on the per tile sequence quality. I suspect that ...
next-gen sequencing written 2.6 years ago by aleka90
0
votes
1
answer
1.4k
views
1
answers
Comment: A: samtools -F 0x2 corrupts the file
... I also tried samtools view -h -b -f 0x2 file.bam > new_file.bam samtools view -h -b -F 0x4 -F 0x8 -F 0x400 -F 0x200 file.bam > new_file.bam but the result that I get from flagstat is: parse error at line 1 [bam_flagstat_core] Truncated file? Continue anyway. 0 + ...
written 3.1 years ago by aleka90 • updated 3.1 years ago by genomax67k
0
votes
1
answer
1.4k
views
1
answers
Comment: A: samtools -F 0x2 corrupts the file
... Thanks both. It have now the correct format. However, I was wondering you might be able to help me clarify something. the results of the samtools flagstat command on the original bam file is: 748518727 + 0 in total (QC-passed reads + QC-failed reads) 47793497 + 0 secondary 0 + 0 suppl ...
written 3.1 years ago by aleka90 • updated 3.1 years ago by genomax67k
5
votes
1
answer
1.4k
views
1
answer
samtools -F 0x2 corrupts the file
... Hello, I have used the following command to extract the properly paired ends from a bam file: samtools view -F 0x2 file.bam > proper_paired.bam but then when I used validateSamFile with picard to validate the bam file with the following command: java -jar /apps/picard-tools/2.1.0/picard.jar Val ...
genome sequence next-gen alignment written 3.1 years ago by aleka90
5
votes
1
answer
2.1k
views
1
answer
bwa -mem log messages
... Hello, I am using bwa mem to aligh paired ends and I get the following errors: [M::process] read 1057202 sequences (80000122 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 440646, 0, 1) [M::mem_pestat] skip orientation FF as there are not enough pairs [M: ...
next-gen alignment sequencing written 3.2 years ago by aleka90 • updated 3.2 years ago by Istvan Albert ♦♦ 80k

Latest awards to aleka

Popular Question 2.2 years ago, created a question with more than 1,000 views. For From Hg18 To Grch38
Popular Question 3.0 years ago, created a question with more than 1,000 views. For From Hg18 To Grch38
Student 3.0 years ago, asked a question with at least 3 up-votes. For From Hg18 To Grch38
Popular Question 5.2 years ago, created a question with more than 1,000 views. For From Hg18 To Grch38

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1215 users visited in the last hour