去除scaffold 上的比对，并且将sam文件转换为bam文件 #! 去除既比对到At同时也比对到Dt上的结果 grep...
1和2步骤中,获得了比对文件后(SAM格式)可进一步转换为BAM格式: samtools view -bS hq_isoforms.fasta.sam > hq_isoforms.fasta.bamsamtools sort hq_isoforms.fasta.bam > hq_isoforms.fasta.sorted.bamsamtools index hq_isoforms.fasta.sorted.bam 二、去冗余 比对文件中记录了低质量比对和同于的基因、转录本...
genecompressionnanoporesampacbiocompressbamfastqgenomic-data-compressioncompression-ratefastq-compressiongtx UpdatedApr 18, 2022 ablab/IsoQuant Star144 Code Issues Pull requests Discussions Transcript discovery and quantification with long RNA reads (Nanopores and PacBio) ...
pbmm2 align --sort$REF$BAM01_polish/aln.bam#pbmm2 index aln.bam# arrow#gcpp --algorithm=arrow -x 5 -X 120 -q 0 -j $THREADS -r $REF aln.bam -o ${REF}.cns.fa,${REF}.cns.fq,${REF}.cns.vcfgcpp -j$THREADS-r$REF01_polish/aln.bam -o 01_polish/${REF##*/}.polish.fa...
--MD Output the MD tag (see the SAM spec).(后面sniffles软件需要MD tag). -t Number of threads CPU线程数. -x STR preset (always applied before other options; see minimap2.1 for details) . 因为minimap2输出的是.sam文件格式,所以使用samtools将.sam转换成.bam,并且使用samtools sort对.bam进行排...
SAM:Sequence Alignment Mapis a generic nucleotide alignment format that describes the alignment of query sequences or sequencing reads to a reference sequence or assembly. (Clickherefor further details.) BAM:Binary version of theSequence Alignment Map (SAM)format. (Clickherefor further details.) ...
因为minimap2输出的是.sam文件格式,所以使用samtools将.sam转换成.bam,并且使用samtools sort对.bam进行排序,然后用samtools index进行索引。上面展示了一步转.bam和分步转.bam的示例。 samtools v1.18版本有--write-index -选项;samtools v1.9版本则没有。
--MD Output the MD tag (see the SAM spec).(后面sniffles软件需要MD tag) -t Number of threads CPU线程数. -x STR preset (always applied before other options; see minimap2.1 for details) . 因为minimap2输出的是**.sam**文件格式,所以使用**samtools**将**.sam**转换成**.bam**,并且使用*...
GPU options: --num-gpus NUM_GPUS Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used. Previousont_germline How would you rate your overall website experience? 1234567 Very dissatisfiedVery satisfied Next Cookie Settings ...
The resulting BAM alignment files were processed to generate capture metrics using the bed files of the tested probe sets (i.e. SMS/PTLS and MHC). For analysis of BAB2714, BAB2695, and BAB3793, PBHoney-Tails [30] (https://www.hgsc.bcm.edu/software/honey) was run with the following ...