Questions tagged [sam]

Use this tag for questions specifically related to the text SAM format. For general questions about the SAM/BAM formats use the tag BAM.

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How can I read multiple different regions from a BAM file in R?

I’m trying to process BAM records (of a coordinate-sorted, indexed BAM file) successively in fixed-size, non-overlapping, sliding genome coordinate windows. Unfortunately I am unable to read records ...
Konrad Rudolph's user avatar
5 votes
0 answers
241 views

convert supplementary reads to primary in sam or bam

I have a problem with a tool, that possibly ignores supplementary reads. I want to find out a bit how this tool works by converting all supplementary reads to primary reads, and then change the names ...
Fini's user avatar
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3 votes
0 answers
722 views

Fastest way to demultiplex bam file based on field

I have a bam file with aligned reads from multiple experiments. For each experiment I have a portion of the sequence identifier, thus for example ...
gc5's user avatar
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2 votes
0 answers
25 views

Off-target % for whole-exome sequencing panel

My samples have been sequenced with the Twist Exome 2.0 sequencing panel, and I want to assess how efficient the sequencing has been. By efficient, I mean examining metrics such as the uniformity (...
kane9530's user avatar
  • 181
2 votes
1 answer
267 views

calculate mismatch frequency/rate from a BAM file

I am working with PAR-CLIP data where experimental procedure induces T to C mismatches. The other types of mismatches we can consider coming from artifact such as PCR errors. It could also be an ...
Ahsan's user avatar
  • 31
2 votes
0 answers
368 views

How to extract reads that map exclusively to a single site with 1 or zero mismatches from BAM files

I generated BAM files (sorted by coordinates) by aligning human RNA reads against the human reference genome using BWA MEM and ...
plicht's user avatar
  • 21
2 votes
0 answers
66 views

Under what circumstances can the SEQ field in a SAM file be a *?

I saw in the SAM format specifications that the SEQ field (10th column) can be a "*" if the sequence is not stored, instead of being the sequence of the mapped read. Under what circumstances ...
Oakheart's user avatar
2 votes
0 answers
122 views

verifybamid results with freemix < 2% and chipmix > 10%

I ran verifyBAMID on each 200 chip-seq BAM files with input merged vcf file of Genotypes of 600 samples ( 200 of them are chip-seq individuals). I had AF,AC,AN in the info column which was calculated ...
GK1610's user avatar
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2 votes
0 answers
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Which R package to use for differential analysis with TPM values?

I'm using hisat2, stringtie tools for the RNA-Seq analysis. After stringtie using ballgown I get FPKM and TPM values for every gene. I have seen that edgeR, Deseq2 can be used for Counts data. I ...
beginner's user avatar
  • 631
1 vote
0 answers
68 views

STACKS ref_map.pl no BAM records

I have 133 aligned and sorted BAM files that I am trying to run through the ref_map.pl script from the STACKS pipeline. My script looks as follows: ...
heather_l's user avatar
1 vote
0 answers
283 views

Extract read names and the associated nucleotides on specific positions from a BAM file (in R)

Let's assume I have a BAM file and several positions that I would like to examine more closely in this alignment. My goal is to find out whether these positions are on the same reads and which ...
wejt's user avatar
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1 vote
0 answers
105 views

Proper scatter/gather of bam files

I'm trying to do some calculus in parallel with BAM files. For that, I need to split the input bam file in chunks, process them in parallel and join them at the end. But I'm facing a read duplication ...
Poshi's user avatar
  • 221
1 vote
0 answers
281 views

How to rename Read Groups

I periodically run into problems with Read Groups. I am in a desperate need for a tool that would allow me to fix them. This time, when I was mapping reads, I formatted all the information in the Read ...
Kamil S Jaron's user avatar
1 vote
0 answers
146 views

How do I Read a Sam File into a String Using ifstream in C++?

I am trying to read a .sam file into a single string in C++. My end goal is to read this string into a vector, where tabs indicate separations between elements of the vector. After making a vector ...
annabelperry's user avatar
1 vote
0 answers
38 views

BAM file filteing to remain best isoform

I ran HiSat2, MarkDuplicate, removed reads with the lower quality score than 40 and finally only kept properly paired reads. After the BAM filtering steps, I used the Scallop results with TransDecoder....
user977828's user avatar
1 vote
0 answers
336 views

bedtools single-nucleotide coverage in BED-specified regions for multiple BAMs

I have a BED6 (BED + name, score, strand info) file that defines some regions of interest. I also have a set of BAMs corresponding to different samples. I would like to obtain output similar to <...
merv's user avatar
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0 votes
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45 views

Generate simulated bam for certain snps

I want to benchmark my DNA sequencing pipeline. In order to do that I want some gold-standard files in every step(.vcf,.bam,.fastq). I want to generate/simulate a bam file of reads for a given set of ...
Shafayet Rahat's user avatar
0 votes
0 answers
45 views

How to export the list of soft-clipped regions from a region of interest in IGV

I want to export the list of soft-clipped regions into a csv file from a region of interest in IGV. Additional information regarding the soft-clipped sequence, coordinate and nucleotide length will be ...
vive's user avatar
  • 1
0 votes
0 answers
96 views

Help sought with GWAS and vcf files, lack phenotype labels

This question has also been asked on Biostars Hi, I am very new to this area, and I am taking a class about bioinformatics. For an independent project assignment, I need to do a GWAS. I am using the ...
user16548's user avatar
0 votes
0 answers
466 views

pysam "Exec format" error

I am a beginner and trying to read a bam file in Python. The lines below throw the error ...
monade's user avatar
  • 11
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0 answers
35 views

Fastest way to count where two bam files are homozygote reference (inverted variant calling)

Maybe I'm having a brain-freeze so excuse me if this is a waste of everyone's time... I am working with an organism with ~700Mb genome. I have bam files of two individuals that are whole genome ...
AWE's user avatar
  • 121
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0 answers
156 views

Splitting .bam files into separate samples for tophat2

I have RNA seq data of 12 samples (paired end, so 24 files) and I ran tophat2 for alignment on all of them which gave me one bam file for all the samples. Now I need separate bam files for all the ...
Dixi Modi's user avatar
0 votes
0 answers
146 views

summarising read group information from a .bam file

I have merged together 2 different .bam files in order to simulate sample contamination. So the reads can come from one of two samples, as shown by the read group info: ...
user438383's user avatar
  • 1,679
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0 answers
36 views

How to visualise /add Arabidopsis T-DNA Lines As Tracks On IGV

We have done some RNA-Seq on Arabidopsis T-DNA lines and mapped the reads on to Arabidopsis genome. Now we wanted to confirm the T-DNA deletion of those lines by loading them on IGV. As a control we ...
Dendrobium's user avatar
0 votes
0 answers
50 views

How to obtain the extended unaligned bases of the read in reference based genome assembly?

I did illumina read mapping based on a particular gene sequence (reference sequence) using the following command, ...
Kumar's user avatar
  • 109
-1 votes
1 answer
99 views

Gviz Coverage Plots

This question has also been asked on Biostars I have two bam files from single-cell RNA sequencing mapped to the reference genome using CellRanger, I can view them in IGV and I have a particular ...
A4747's user avatar
  • 1