Hello everyone!
I'm new to bioinformatics.
I have some questions about reading (eye-balling) a .sam file.
For example:...
17 results in 0.0057 seconds.
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How can I dissect .sam files in text editor??
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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.... -
CIGAR inconsist with read length. Does Bowtie2 reedit read sequence?
Hi, guys
I used bowtie2 to align paired-end reads to hg19 genome, and got the sam format output. Then when I tried to convert the sam into...Last edited by wisense; 05-24-2015, 11:03 PM. -
How does BWA identify PCR duplicates correctly?
Does it use the usual "same-start-position-for-both-paired-ends" approach? If so, why do many users do this check manually or use picard and... -
[Bowtie2] CIGAR string calculation.
Hi All,
The SAM output gives the 1-based leftmost mapping POSition of the first matching base of the reference. I am wondering if it is... -
Single position mismatch agglomerate after alignment
Hello folks,
After downloading and realigning the reads of the ChIP-seq sample GSM721212 with bwa, I get a quite strange mismatch profile... -
How does bedtools - bamToBed handle S operation in cigar string?
Hi,
I've been recently using bamToBed utility from the bedtools suite in order to transform the alignments in a BAM file into features... -
CIGAR and Sequence length incosistent
Hello,
I am trying to convert a .sam file into .bam file and I get the following error:
CIGAR and Sequence length are inconsistent.... -
gatk countcovariate ERROR MESSAGE Read starting with deletion. Cigar: 1D22M1I71M8S
Hello,
I received targeted sequence reads from a 454 machine.
In my way on the application of the GATKV3.0 best practice guideline,... -
SAM/CIGAR for deletion before first match
Hi all,
This is my first post here. Just searching this site has answered so many questions I've had previously, but I can't find an answer to... -
CAGE tags
Hi Everybody!
My problem is about mapping where only the location of 5'end of the read is meaningful, rest of the sequence is needed only...Last edited by LukaszKielpinski; 03-19-2012, 01:11 PM. -
samtools: bam_pileup.c:112: resolve_cigar2: Assertion `s->k < c->n_cigar' failed
Hi,
I have a bam file that I have run through the GATK pipeline (i.e. de novo realignments around indels, duplicates removed and quality... -
The 'S' in CIGAR of sam file (bwa)
the S means "soft clipping (clipped sequences present in SEQ)".
but I saw an example of CIGAR which is "72M28S" (4mismatch),and... -
bowtie - invalid CIGAR string - wrong sam format
Hi,
I am trying to align short reads from Illumina with different aligners.
I have used the same .fq files to align with BWA,... -
how to get perfects aligned reads instead of real read
Hi,
Is there any way to modify a SAM/BAM in order to have real reads replaced by the perfect reads(replacing wrong bases with the right bases in...
