Open z626093820 opened 1 year ago
When I use hisat2 comparison software, the comparison rate is high, why is it
It could be an issue with pairing of reads in FASTQ files. You can test it by mapping Read1 and Read2 separately.
It could be an issue with pairing of reads in FASTQ files. You can test it by mapping Read1 and Read2 separately.
When I map the Read1 and Read2 files separately, the map rate of the two files reaches more than 80%,how can i slove the problem about the pairing of reads in FASTQ files? THANK YOU
If you are trimming reads before mapping, I would try to map untrimmed (raw) reads.
If you are trimming reads before mapping, I would try to map untrimmed (raw) reads.
When I analyze the new command parameters given by the sequencing company, the mapping rate has reached 70%. Excuse me, which of these parameters have played a key role?THANK YOU!
the low mapping rate command : STAR --runThreadN 15 --runMode alignReads --quantMode TranscriptomeSAM GeneCounts --sjdbOverhang 149 --twopassMode Basic --outSAMtype BAM SortedByCoordinate --outBAMsortingThreadN 15 --limitSjdbInsertNsj 12115510 --genomeDir /storage/zuozd/genome/ipomoea_batatas_tai6/star-gffreadgtf149/ --readFilesIn /storage/zuozd/20230921bleeding_sap/00cleandata/${i}_1.clean.fq.gz /storage/zuozd/20230921bleeding_sap/00cleandata/${i}_1.clean.fq.gz --readFilesCommand zcat --outFileNamePrefix ${i}
the high mapping rate command: STAR --runThreadN 15 --runMode alignReads --readFilesCommand zcat --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNmax 2 --outReadsUnmapped Fastx --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 --chimOutJunctionFormat 1 --genomeDir /storage/zuozd/genome/ipomoea_batatas_tai6/star-gffreadgtf149/ --readFilesIn /storage/zuozd/20230921bleeding_sap/00cleandata/L58-1_1.clean.fq.gz /storage/zuozd/20230921bleeding_sap/00cleandata/L58-1_2.clean.fq.gz --outFileNamePrefix L58-1
When I use STAR for alignment, many reads do not align. How can I resolve this? THANK YOU !
below is my parameter:
STAR --runThreadN 15 --runMode alignReads --quantMode TranscriptomeSAM GeneCounts --sjdbOverhang 149 --twopassMode Basic --outSAMtype BAM SortedByCoordinate --outBAMsortingThreadN 15 --limitSjdbInsertNsj 12115510 --genomeDir /storage/zuozd/genome/ipomoea_batatas_tai6/star-gffreadgtf149/ --readFilesIn /storage/zuozd/20230921bleeding_sap/00cleandata/${i}_1.clean.fq.gz /storage/zuozd/20230921bleeding_sap/00cleandata/${i}_1.clean.fq.gz --readFilesCommand zcat --outFileNamePrefix ${i}