FASTA and FASTQ formats are both file formats that contain sequencing reads while SAM files are these reads aligned to a reference sequence. In other words, FASTA and FASTQ are the "raw data" of sequencing while SAM is the product of aligning the sequencing reads to a refseq. A FASTA file contains a read name followed by the sequence.

2017年6月27日 · samtools merge merged.bam s1.sort.sam s2.sort.sam s3.sort.sam If there are multiple input files that share the same read group, then by default they will have random strings appended to make the read groups unique. This can be stopped by using the -c option, as mentioned in man samtools merge:

I have a text file 'qnames.txt' with QNAMEs in the following format: EXAMPLE:QNAME1 EXAMPLE:QNAME2 EXAMPLE:QNAME3 EXAMPLE:QNAME4 EXAMPLE:QNAME5 I would like to subset my BAM file.bam via all of these QNAMEs into a new SAM. Naturally, I can do this individually, e.g. samtools view file.bam | grep 'EXAMPLE:QNAME1' > subset.bam

2021年6月3日 · Mapping Information from SAM/BAM file. 3. Parsing SAM/BAM files for additional information. 4.

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2021年1月26日 · I have 10 .sam files after my bowtie2 alignment on ten single-pair sequences. I would like to build a graph based on that output data, however I don't see any other solution but just writing the alignment percentage manually after each iteration. Is there a tool that can help me to build a .csv file so I can manipulate the output data more easily?

2022年2月3日 · Not only will you save disk space by converting to BAM, but BAM files are faster to manipulate than SAM. Source: Dave Tang's SAMTools wiki. sort supports uncompressed SAM format from a file or stdin, though index requires BGZIP-compressed SAM or BAM. I don't think you can get around this.

htsbox samview -p in.bam | less -S htsbox samview -pS in.sam | less -S It outputs mapping positions in the PAF format, which looks something like: read1 4983 774 4982 + chr18 80373285 26911072 26915544 3835 4631 60 \ mm:i:214 io:i:119 …

2020年10月26日 · I imagined the .sam file already contains the information about the assembly used to produce it. If I'm wrong, I'm sorry and please correct me, I'm just assuming. What I want to do is, for each read in the .sam file, I find out its position in the assembled scaffold, and I record, Read_ID,Scaffold_ID,Read_Position_Inside_Scaffold,RX,BC

2021年11月18日 · input paired end FASTQ files (human) into SPAdes to create contigs.fasta file; align paired end FASTQ files to contigs.fasta file with minimap2 to get SAM file; convert SAM to BAM with samtools; sort and index BAM file; load BAM …