Hello everyone!
I'm new to bioinformatics.
I have some questions about reading (eye-balling) a .sam file.
For example:...
10 results in 0.0032 seconds.
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How can I dissect .sam files in text editor??
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bowtie2 bit 2 of the flag
Hello,
I am wondering what does mean "The second bit (2 in decimal, 0x2 in hexadecimal) is set if the read is part of a pair that... -
All SAM alignments on reverse strand
I just went through my first TopHat analysis, and am worried about the output. There are actually two things that concern me:
1. The bitwise... -
Problem compiling bcl2fastq-1.8.4
Hello!
I am trying to compile bcl2fastq on a server where I cannot be root and should be installed in a specific folder (server is under... -
samtools fixamte appears to be doing nothing
I have to do some filtering of reads in BAM alignments based on mapping quality but also to remove some reads that overlap certain regions of the reference... -
How can I filter out reads who or whose pairs are unmapped in samtools?
How can I filter out reads who or whose pairs are unmapped in samtools?
I tried using "samtools view -F 4 -F 8 SAMFILE". However,... -
Bowtie2 Inspect output flags
I used Bowtie2 to build an index for a single human chromosome for subsequent RNA Seq analysis, as that’s all I’m interested in right now, and I figured... -
BWA conflicting flags
Hi!
I have a problem, and haven't found a solution for it, maybe someone in here might be able to help me. I have some hiseq reads and was mapping... -
Tophat ignoring '--max-multihits' flag?
Hi,
I tried to exclude reads that map to multiple locations using the flag mentioned above. The run.log file shows this. However, the following... -
strand of query and mate
Hi everybody,
I'm performing downstream pair-end analysis on Genome Analyzer II data. The reads was aligned against a reference genome...
