20 results in 0.0624 seconds.
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TLEN field explained
If the TLEN value is Zero; it means information is unavailable, (I think this means that the alignment does not make sense from biological point if view...Last edited by Medhat; 09-28-2018, 11:08 AM. -
Help in output only the alignments identical to the reference
Hello everyone,
I have a SAM file resulting from a STAR alignment, containing reads aligned to a reference of smallRNA sequences (I created the... -
Header missing from .bwt -> .sam conversion
I am using bowtie and have been outputting .bwt files but now need to convert those files to .sam format. I know bowtie has a .sam output option (-S)... -
Separating a .sam or .bam file that is based on alignment to multiple sequences
Hey people!
I have the following setup. I have a .sam file based on the alignment of E.coli genome reads to a multifasta file containing the sequences... -
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... -
Sam quality flag
Hello all,
heading just a quick reply
I aligned my color-space fastq by bowtie 1 and got sam as output. But in my all mapped... -
How to filter a SAM/BAM file by bp
Hi community,
I want to filter my SAM/BAM files to just keep my transcripts above 1000bp. What I am doing now is to convert my SAM/BAM... -
bwa-mem -C option problem with barcode field in SAM file
I recently started working bwa-mem on a 2X100 PE RNAseq dataset (ILMN cassava 1.8+) and ran into some problems with the sam/bam headers, as well as the... -
a general question on DEXSeq data preparations
I was following the steps in the vignette of DEXSeq here to construct the exon count files (.txt) for each of my 16 biological samples. However, as shown... -
Cufflinks refuses to operate on Tophat2 created bam or sam files due to sorting error
Hi there,
I have really had alot of trouble over the last couple weeks trying to get either Cufflinks 2.0 and 2.1 to accept Tophat 2 (latest... -
How BWA and Bowtie mention unique reads in SAM files?
Hello everybody,
I am trying to figure how BWA and Bowtie define a read as unique.
Making here an algorithm to decide if a read... -
LAST output as SAM/BAM
Im testing the sequence read mapping LAST (http://last.cbrc.jp/) But this program only outputs MAF alignment files. I tried using https://github.com/... -
samtools view -f 4 inconsistency
Hi,
I want to select unmapped reads in my bam file generated by bwa. When I use samtools view -f 4, it also selects some reads with flag... -
Not report promiscuous reads in bowtie
Hi,
I was wondering if there is a way in bowtie to stop further alignment of short reads that have already mapped to more than a certain number... -
delete reads that dont overlap with any other reads
Hi,
I am a beginner to this area. I have an alignment file in bam/sam format after aligning short reads to my genome of interest using bowtie....
