Rsamtools Scanbam()
When you are using scanBam() to parse through a BAM file, is there an option to extract the entire read line. i.e. instead of specifiying "what" you want to see, can you just pull the entire line from the BAM file?
parsing
bam
• 2,126 views
•
link
written
by
bic.uwaterloo.ca •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How To Sort Sam File
written by Chen Sun<p>I want to process the <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a> file created by <a href='http://bio-bwa.sourceforge.net/'>BWA</a>, if it is sorted by the sequence coordinate on reference, it will be …
-
Sam To Bam - Loss Of Data Or Just Great Compression?
written by Clare<p>I use picard tools to take a <a href='http://bio-bwa.sourceforge.net/'>BWA</a> alignment <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a> file and convert it into a sorted <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> file. Normally this works …
-
Removing Phix Data From Ngs Data For Analysis
written by crivenster<p>I have a NGS data containing 95-98% of PHIX data,which i dont need. So after some reading, I used <a href='http://bio-bwa.sourceforge.net/'>BWA</a> to align the reads …
-
Merging Bam Files
written by rickyflintoff •<p>I have two <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> files that have a different sample in read group (@RG) section. I would like the sample to be the same. …
-
Error In Converting Sam To Bam By Samtools
written by Raghav<p>hello every one,</p> <p>after mapping,i encountered an error during converting my <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a> out file into <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> out put file.</p> <p>[cdac@nbri <a href='http://samtools.sourceforge.net/'>samtools</a>-0.1.19]$ <a …
-
How Do I Pull Out One Read (Given Its Id) From A Bam?
written by zam.iqbal.genome<p>Hi there</p> <p>Does anyone know how I can pull just one read from a <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> file, when I know the read-id (and sequence) of …
-
Chip-Seq Peak Calling Using Macs For Replicates In Galaxy
written by anon111 •<p>I'm new to Galaxy. I have Chip-seq data for two cell types. Each cell type has two replicates. I already ran an alignment workflow in …
-
Running A Somatic Sniper With Marked Duplicate And Sorted Bam File.
written by kulkarni.aishwarya87 •<p>Hi for running the <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> file through somatic sniper, do we need a marked duplicate <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> file? Thanks</p>
-
B/Sam To Fasta In R
written by laemtao •<p>I'm looking for a way in Bioconductor to convert a <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> file to a filtered fasta file. </p> <p>Currently, I've come across two methods …
-
Sam To Bam Conversion Reference Fasta File
written by Atom Smasher •<p>Hello,</p> <p>I had some data in "eland_export.txt" format and I want to convert it to the <a href='http://samtools.sourceforge.net/SAM1.pdf'>SAM</a> format first and then later to the …