Hi,
I'm trying to align a fastq.gz file with bowtie.
My script is:
${bowtie_source} --sam --best ${ref_genome} ${fastq_file}...
127 results in 0.0043 seconds.
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Alignment with bowtie doesn't creates .sam file
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Paired end SAM to single end
I am performing PAR-CLIP which is typically done using single end however we ran paired because it fit in with our in house set up.
I've... -
BWA sam -> bam in pipeline
I am trying to use BWA mem to align pair-end reads to a single genome and pipe the sam file output to a bam and then a bedfile. The pipeline doesn't seem... -
Read direction lost with BWA in SAM output?
I've tried two different header styles in my input FASTQ headers when running BWA:
@SN7001163:162:C4A1UACXX:1:1101:1062:2076/1
... -
How can I dissect .sam files in text editor??
Hello everyone!
I'm new to bioinformatics.
I have some questions about reading (eye-balling) a .sam file.
For example:... -
Webinar: Sequence alignment: the central step in reference based NGS data analysis
Greetings from Persistent LABS !!
Join us for the third webinar of our series on "Sequence alignment: the central step in reference... -
Mapping possition in SAM format
Hi all,
I have question concerning the SAM format. I need to define position of read mapped to the reference. Which means position of first base... -
replacing CIGAR string
Hello,
I want to replace the CIGAR strings of SAM/BAM file without changing anything else so that the soft-clipped bases are shown as matches/mismatches.... -
Bug with eXpress: Unable to open input SAM file
Dear all ,
I tried to use eXpress to count the mapping results obtained with Bowtie2.
The command used is
express -m 450... -
sam format: SEQ field
Hi
I have a question regarding SAM format. What does it represent the field $10 (SEQ)? Checking SAM format manual (https://samtools.g... -
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... -
Is there a difference between a .sam produced by tophat2 and bowtie2?
I hope this makes sense,
So I have a perl script that is written to take the accepted_hits.bam file from tophat2, in sam format as an input....Last edited by meabh; 05-24-2016, 06:51 AM. Reason: I didn't realise you could output sam file from tophat2 which makes the question redundant -
MAPping Quality v.s. Alignment Score (AS) in SAM format
MAPQ: MAPping Quality. It equals −10 log10 Pr{mapping position is wrong}, rounded to the nearest
integer. A value 255 indicates that the... -
how use bowtie2 output sam file for magan5 input
I'm new to bioinformatics and I need to know how can I use bowtie2 output .sam file to megan5 to view polytechnic tree of microbes.I use Silva DB as reference... -
Difference between sequence coverage and physical coverage
Hi to everyone,
I'm looking to understand the difference between these two kinds of coverage:
Sequence Coverage and Physical...
