User: Swbarnes2

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Swbarnes21.5k
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Posts by Swbarnes2

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Answer: A: Cuffdiff Says Sam Isn'T Sorted, Although It Handled It Cufflinks
... It doesn't think you have a .bam file. That's a bigger problem than the lack of sorting. ...
written 7.7 years ago by Swbarnes21.5k
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Answer: A: Bwa Sampe Very Large Insert Size
... 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 7.7 years ago by Swbarnes21.5k
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Detecting Trace Contamiants In Sanger Sequencing
... 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 ...
sanger sequencing written 7.7 years ago by Swbarnes21.5k • updated 7.7 years ago by Darked894.2k
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Answer: A: Mapping Reads Back To Assembly Contigs To Generate Pileup
... They might have trimmed out more low-quality reads or repetative reads than you did. ...
written 7.7 years ago by Swbarnes21.5k
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Comment: C: Convert Bam To Fastq With Pe & Se Reads
... 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 7.7 years ago by Swbarnes21.5k
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Answer: A: Convert Bam To Fastq With Pe & Se Reads
... 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 7.7 years ago by Swbarnes21.5k
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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 7.7 years ago by Swbarnes21.5k
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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 7.7 years ago by Swbarnes21.5k
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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 7.7 years ago by Swbarnes21.5k
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Answer: A: Samtools Mpileup Directional Coverage
... 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 7.7 years ago by Swbarnes21.5k

Latest awards to Swbarnes2

Guru 7.7 years ago, received more than 100 upvotes.
Teacher 7.8 years ago, created an answer with at least 3 up-votes. For A: How To Tell How Well A Sam File Was Mapped
Teacher 7.9 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 8.0 years ago, created an answer with at least 3 up-votes. For A: How To Annotate A Human Dna Position
Appreciated 8.0 years ago, created a post with more than 5 votes. For A: Understanding Vcf File Format
Good Answer 8.0 years ago, created an answer that was upvoted at least 5 times. For A: Understanding Vcf File Format
Teacher 8.0 years ago, created an answer with at least 3 up-votes. For A: Understanding Vcf File Format
Teacher 8.0 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
Teacher 8.0 years ago, created an answer with at least 3 up-votes. For A: Samtools Idxstats
Good Answer 8.0 years ago, created an answer that was upvoted at least 5 times. For A: Samtools Idxstats
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Appreciated 8.3 years ago, created a post with more than 5 votes. For A: Can´T Find The Snps With Samtools (Only Get Indels)
Teacher 8.3 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 8.3 years ago, created an answer that was upvoted at least 5 times. For A: Can´T Find The Snps With Samtools (Only Get Indels)
Teacher 8.3 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
Teacher 8.3 years ago, created an answer with at least 3 up-votes. For A: Raw Illumina Data
Teacher 8.4 years ago, created an answer with at least 3 up-votes. For A: Oligonucleotide Vs K-Mer
Appreciated 8.4 years ago, created a post with more than 5 votes. For A: Oligonucleotide Vs K-Mer
Good Answer 8.4 years ago, created an answer that was upvoted at least 5 times. For A: Oligonucleotide Vs K-Mer
Teacher 8.4 years ago, created an answer with at least 3 up-votes. For A: Mapping Rates From Bwa
Teacher 8.5 years ago, created an answer with at least 3 up-votes. For A: Genomic Alignment And Snp/Indel Calling - My First Ever "Pipeline"

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