Hisat2 aligned concordantly exactly 1 time

Author: piqu

August undefined, 2024

Webb17 apr. 2024 · many reads aligned discordantly 1 time · Issue #291 · DaehwanKimLab/hisat2 · GitHub DaehwanKimLab / hisat2 many reads aligned discordantly 1 time #291 Open soleilll opened this issue on Apr 17, 2024 · 0 comments soleilll commented on Apr 17, 2024 Sign up for free to join this conversation on GitHub . … 本文具体解释部分（一）中内容复制自 Biostar 内容，后面附上我实际的例子，二者略有不同，整体理解上没大问题，有不合适之处可联系我。 Visa mer

How to understand Hisat2 aligment result - Biostar: S

Webb28 mars 2024 · HISAT2 mapping. hi everybody, I have a question about discordant alignment results. 23250959 reads; of these: 23250959 (100.00%) were paired; of … Webb在参数--fr下：前两种比对就是合理比对，也即：concordantly，后两种比对会成为不合理比对，也即：aligned discordantly，如果两个reads距离太远也会成为不合理比对。. 2. Multiple alignments 多重比对. 2.1.定义：一对reads或一个pair比对上genome的多个位置，也即：aligned >1 times 或是aligned concordantly >1 times，这对reads ... kvgfort gmail.com

HiSAT2 RNAseq alignment low + stranded data predicted to

Webb29 aug. 2015 · 572503 (8.49%) aligned concordantly 0 times 5478092 (81.24%) aligned concordantly exactly 1 time 692450 (10.27%) aligned concordantly >1 times----572503 pairs aligned concordantly 0 times; of these: 35260 (6.16%) aligned discordantly 1 time----537243 pairs aligned 0 times concordantly or discordantly; of these: 1074486 … Webb23 mars 2024 · concordMapRate: concordance mapping rate as reported by HISAT2 (adding those that aligned concordantly exactly 1 time and more than 1). totalMapped: reads that map to chrs 1 to 22, X, Y. Calculated using derfinder::getTotalMapped() on the resulting BAM files (we convert the HISAT2 SAM file to BAM). mitoMapped: reads that … WebbI am getting some interesting behavior with the HiSat2 alignment percentages. When the Report alignments tailored specifically for Cufflinks option is checked in galaxy or the … kvh 1760 connect to computer

Alignment QC differences between HISAT2 and Qualimap

Webb11 mars 2016 · [B]hisat2[/B] 33778368 reads; of these: 33778368 (100.00%) were paired; of these: 32551450 (96.37%) aligned concordantly 0 times 564637 (1.67%) aligned concordantly exactly 1 time 662281 (1.96%) aligned concordantly >1 times ---- 32551450 pairs aligned concordantly 0 times; of these: 20823 (0.06%) aligned … http://daehwankimlab.github.io/hisat2/manual/ pro-gym fitness campWebb20 mars 2024 · 定义：一对reads/一个pair比对上genome的多个位置，也即： aligned >1 times 或是 aligned concordantly >1 times ，这对reads/这个pair就会成为多重比对。 … kvg mechatronics

"Webb15 juni 2024 · HISAT2 is the fastest spliced mapper currently available. It is part of the new tuxedo suite of tools and it will map RNA-Seq data to the genome as well as identify splice junctions. HISAT2, like BWA and bowtie, uses burrows-wheeler transform (BWT) to compress genomes such that they require very little memory to store. " - Hisat2 aligned concordantly exactly 1 time

Hisat2 aligned concordantly exactly 1 time

The rate of "aligned concordantly exactly 1 time" in Hisat2

Webb4 sep. 2024 · Aligned 1 time: 868436 (41.40%) Aligned >1 times: 72463 (3.45%) And here's the results without --repeat: HISAT2 summary stats: Total pairs: 29939629 Aligned concordantly or discordantly 0 time: … Webb17 apr. 2024 · many reads aligned discordantly 1 time · Issue #291 · DaehwanKimLab/hisat2 · GitHub DaehwanKimLab / hisat2 many reads aligned …

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Webb20 sep. 2024 · After indexing the genome, I used hisat2 to do the alignment for raw RNA-seq data. As my samples actually have some foreign genomic segments compared to …

Webb9 apr. 2024 · In alignment summary statistics, the indentations are useful to break down the total. For example, 11889751 (total paired reads) is a total of 1298966 (aligned concordantly 0 times), 9865016 (aligned concordantly exactly 1 time), and 725769 (aligned concordantly >1 times). Enhance your skills with courses on genomics and … Webb1001435 (14.95%) aligned >1 times. 88.21% overall alignment rate. the Bowtie2 result summary is divided in 3 sections: Concordant alignment - In your data (4522376 + …

Webb17 apr. 2024 · I ran HiSAT2 three times on one of the samples' pairs of reads with the following options (-fr, ... 5629996 (91.02%) aligned concordantly 0 times 475008 (7.68%) aligned concordantly exactly 1 time 80149 (1.30%) aligned concordantly >1 times ---- 5629996 pairs aligned concordantly 0 times; of these: 1575716 ... Webb18 maj 2024 · HISAT2 reads aligned concordantly exactly 1 time. 06-15-2016, 03:31 PM. Hi all, I am currently using HISAT2 to do read mapping. After having the mapped …

Webb7 mars 2024 · Extract reads aligned concordantly exactly 1 time from hisat2 output (.sam file) · Issue #358 · DaehwanKimLab/hisat2 · GitHub DaehwanKimLab / hisat2 …

WebbI used hisat2 for aligning reads to to the genome. I have an alignment summary for sample1 as follows: 89038751 reads; of these: 89038751 (100.00%) were paired; of these: 5641019 (6.34%) aligned concordantly 0 times 67665552 (76.00%) aligned concordantly exactly 1 time 15732180 (17.67%) aligned concordantly >1 times ---- … kvg online ticketWebbAlignment QC differences between HISAT2 and Qualimap. I used hisat2 for aligning reads to to the genome. I have an alignment summary for sample1 as follows: 89038751 … kvh 1775 technical manualWebb20 sep. 2024 · 28118821 reads; of these: 28118821 (100.00%) were paired; of these: 1501351 (5.34%) aligned concordantly 0 times 25510596 (90.72%) aligned concordantly exactly 1 time 1106874 (3.94%) aligned concordantly >1 times ---- 1501351 pairs aligned concordantly 0 times; of these: 55070 (3.67%) aligned … pro-growth turf and treeWebb27 juli 2024 · mapped reads number的另一种计算方法：concordantly exactly 1 time(14853850)，aligned concordantly >1 times(3509724)，aligned concordantly … pro-hatsWebb1. Align the RNA-seq reads to a reference genome. In the left tool panel menu, under NGS Analysis, select NGS: RNA Analysis > HISAT2 and set the parameters as follows: Source for the reference genome to align against: Use built-in genome. Select a reference genome: Fruit Fly (Drosophila melanogaster): dm3. kvg wutha farnrodaWebb24 sep. 2024 · 31445543 (99.75%) aligned concordantly 0 times 2010 (0.01%) aligned concordantly exactly 1 time 77694 (0.25%) aligned concordantly >1 times ---- 31445543 pairs aligned concordantly 0 times; of these: 20260019 (64.43%) aligned discordantly 1 time ---- 11185524 pairs aligned 0 times concordantly or discordantly; … pro-hawk corporationWebb30 jan. 2024 · I map pair end read using Hisat2 to genome: [root@psgl hisat2] ... aligned concordantly exactly 1 time 49541361 (49.03%) aligned concordantly >1 times ---- 6478970 pairs aligned concordantly 0 times; of these: 338196 (5.22%) aligned discordantly 1 time ---- 6140774 pairs aligned 0 times concordantly or discordantly; … pro-hand fronty