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.
26
questions with no upvoted or accepted answers
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484
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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 ...
- 4,845
5
votes
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answers
241
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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 ...
- 153
3
votes
0
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722
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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
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- 1,783
2
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25
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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 (...
- 181
2
votes
1
answer
267
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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 ...
- 31
2
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0
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368
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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 ...
- 21
2
votes
0
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66
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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 ...
- 21
2
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122
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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 ...
- 21
2
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2k
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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 ...
- 631
1
vote
0
answers
68
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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:
...
- 31
1
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0
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284
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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 ...
- 11
1
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105
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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 ...
- 221
1
vote
0
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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 ...
- 5,542
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 ...
- 309
1
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0
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38
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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....
- 453
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 <...
- 651
0
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45
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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 ...
- 295
0
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45
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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 ...
- 1
0
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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 ...
0
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0
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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
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- 11
0
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35
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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 ...
- 121
0
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156
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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 ...
0
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146
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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:
...
- 1,679
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36
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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 ...
- 187
0
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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,
...
- 109
-1
votes
1
answer
99
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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 ...
- 1