User: Swbarnes2
Swbarnes2 • 1.5k
- Reputation:
- 1,490
- Status:
- Trusted
- Location:
- Last seen:
- 8 years, 11 months ago
- Joined:
- 10 years ago
- Email:
- u1364
Posts by Swbarnes2
<prev
• 100 results •
page 1 of 10 •
next >
0
votes
4
answers
10k
views
4
answers
... It doesn't think you have a .bam file. That's a bigger problem than the lack of sorting. ...
written 8.9 years ago by
Swbarnes2 • 1.5k
0
votes
2
answers
4.2k
views
2
answers
... bwa will also do that if you screwed up your command line, and mistyped the name of an input file in a previous step. If you mistyped the name of your fastq in the aln step, I think you still make a .sai file, and sampe will do its best on what it has. So that's a quick thing you can double-check. ...
written 8.9 years ago by
Swbarnes2 • 1.5k
2
votes
1
answer
1.9k
views
1
answer
... I've got many 96-well plates of samples (a library of vectors with various insert sequences, one per well), and they know that some of the wells are cross-contaminated. They are hoping to be able to distingush which wells have < 1% contamination. They have sanger end reads of each wells, coveri ...
0
votes
2
answers
2.7k
views
2
answers
... They might have trimmed out more low-quality reads or repetative reads than you did. ...
written 8.9 years ago by
Swbarnes2 • 1.5k
2
votes
3
answers
6.8k
views
3
answers
... What's so onerous about running samtools view 3 times to split up the .bam into those three groups?
samtools view -bf 64 mixed.bam > read1.bam
samtools view -bf 128 mixed.bam > read2.bam
samtools view -bF 1 mixed.bam > SE.bam
Then run bam2fastq on each of those files.
...
written 8.9 years ago by
Swbarnes2 • 1.5k
3
votes
3
answers
6.8k
views
3
answers
... You could use samtools view to filter the .bam into three files; reads that are read 1, reads that are read 2, and reads from SE experiments. Picard can sort each .bam by read name, before you convert them to fastq. ...
written 8.9 years ago by
Swbarnes2 • 1.5k
1
vote
2
answers
5.4k
views
2
answers
Answer:
A: Sam Tools Pileup Format
... Instead of running a separate program to convert fastq to fasta, vcfutils.pl is easy enough to alter. It's a perl script, so it's a flat text file. Basically, you want the last few lines of vcf2fq to look like this:
print "\>$chr\n"; &v2q_print_str($seq);
# print "+\n"; &v2q_print_st ...
written 8.9 years ago by
Swbarnes2 • 1.5k
0
votes
2
answers
3.3k
views
2
answers
Comment:
C: Markduplicates Error
... Look at a little of the orignal .sam file with your eyeballs. What flags do you see? Is your pipeline possibly changing those flags? ...
written 8.9 years ago by
Swbarnes2 • 1.5k
1
vote
2
answers
3.3k
views
2
answers
Answer:
A: Markduplicates Error
... It looks like the software that made your .bam made the flags wrong. It looks like Picard is complainnig that your .bam entries have the 1 flagged, but not 64 or 128.
But as long as your read names are identical between the two reads, Picard might still be able to figure out that they are paired, a ...
written 8.9 years ago by
Swbarnes2 • 1.5k
0
votes
3
answers
2.6k
views
3
answers
... If you want to count across the whole .bam, use samtools flagstat
samtools flagstat -cf 16 -F 4
will count how many mapped reads run in the reverse direction.
samtools flagstat -cF 20
will count how many mapped reads run in the forward direction.
The pileup will work too, periods means forward di ...
written 8.9 years ago by
Swbarnes2 • 1.5k
Latest awards to Swbarnes2
Guru
8.9 years ago,
received more than 100 upvotes.
Teacher
9.0 years ago,
created an answer with at least 3 up-votes.
For A: How To Tell How Well A Sam File Was Mapped
Teacher
9.1 years ago,
created an answer with at least 3 up-votes.
For A: Why Do We Align Each Pair Set Separately In An Illumina Paired End Sequencing St
Teacher
9.2 years ago,
created an answer with at least 3 up-votes.
For A: How To Annotate A Human Dna Position
Appreciated
9.2 years ago,
created a post with more than 5 votes.
For A: Understanding Vcf File Format
Good Answer
9.2 years ago,
created an answer that was upvoted at least 5 times.
For A: Understanding Vcf File Format
Teacher
9.2 years ago,
created an answer with at least 3 up-votes.
For A: Understanding Vcf File Format
Teacher
9.3 years ago,
created an answer with at least 3 up-votes.
For A: In The Various Dna Sequencing Methods What Restricts The Process From Sequencing
Good Answer
9.3 years ago,
created an answer that was upvoted at least 5 times.
For A: Samtools Idxstats
Teacher
9.3 years ago,
created an answer with at least 3 up-votes.
For A: How Do You Explain What You Do To The Guy On The Street Or Your Mum?
Appreciated
9.5 years ago,
created a post with more than 5 votes.
For A: Can´T Find The Snps With Samtools (Only Get Indels)
Teacher
9.5 years ago,
created an answer with at least 3 up-votes.
For A: Can´T Find The Snps With Samtools (Only Get Indels)
Good Answer
9.5 years ago,
created an answer that was upvoted at least 5 times.
For A: Can´T Find The Snps With Samtools (Only Get Indels)
Appreciated
9.5 years ago,
created a post with more than 5 votes.
For A: How To Differentiate Between Mate Pair And Paired End Reads Based On Sam Flag
Teacher
9.5 years ago,
created an answer with at least 3 up-votes.
For A: How To Differentiate Between Mate Pair And Paired End Reads Based On Sam Flag
Good Answer
9.6 years ago,
created an answer that was upvoted at least 5 times.
For A: Oligonucleotide Vs K-Mer
Teacher
9.8 years ago,
created an answer with at least 3 up-votes.
For A: Genomic Alignment And Snp/Indel Calling - My First Ever "Pipeline"
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1625 users visited in the last hour