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cougarlj / COMPSRA

COMPSRA: a COMprehensive Platform for Small RNA-Seq data Analysis
https://regepi.bwh.harvard.edu/circurna/
GNU General Public License v3.0
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What dose the InCluster mean in the annotation file of pirna #35

Closed liangwx332 closed 2 years ago

liangwx332 commented 2 years ago

Hi

I used COMPSRA to gain the finally result of pirna, but I did not know the mean of InCluster in the last column.

The results as following

DB Name ID Count InCluster piRNABank|piRBase hsa_piR_016658 DQ592931 74058 false piRNABank|piRBase hsa_piR_016659 DQ592932 22284 false piRNABank|piRBase hsa_piR_010541 DQ584197 2 false piRBase piR-hsa-32235 - 6618 false piRBase piR-hsa-26508 DQ596292 2100 false piRBase piR-hsa-32236 - 31 true piRNABank|piRBase hsa_piR_004506 DQ576200 2 false piRNABank|piRBase hsa_piR_006308 DQ578624 1 false

cougarlj commented 2 years ago

Dear liangwx332,

The InCluster column comes from the database piRNAclusterDB in which the author defined piRNAs should be in clusters. So, false means this piRNA is not in the clusters defined in piRNAclusterDB and true means yes. You can refer to the original paper of piRNAclusterDB. Currently, COMPSRA uses the 1.0 version of piRNAclusterDB.

Best Wishes, Jiang Li

liangwx332 commented 2 years ago

Dear liangwx332,

The InCluster column comes from the database piRNAclusterDB in which the author defined piRNAs should be in clusters. So, false means this piRNA is not in the clusters defined in piRNAclusterDB and true means yes. You can refer to the original paper of piRNAclusterDB. Currently, COMPSRA uses the 1.0 version of piRNAclusterDB.

Best Wishes, Jiang Li

Hi,

Thank you very much for your help

Best wishes, Liang Wei

liangwx332 commented 2 years ago

Hi，

I have an another question. Because speed of downloading star and hg38 genome is slow. So I could use my star to construct index, then use my star to align to genome but alignment parameters provided by your, finally use your scripts to annotation the alignment results. Code as following

Buildind indexes : STAR --genomeDir . --genomeFastaFiles hg38.fa --runMode genomeGenerate --runThreadN 3

Alingment: STAR --runThreadN 4 --runMode alignReads --outSAMtype BAM Unsorted --outSAMattributes Standard --readFilesCommand zcat --outSAMunmapped Within --outReadsUnmapped None --alignEndsType Local --outFilterMismatchNmax 1 --alignIntronMax 1 --alignIntronMin 2 --outFilterMultimapScoreRange 1 --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterMultimapNmax 1000000 --genomeDir /home/liangwei/project/1.pimran/index/test --readFilesIn /home/liangwei/project2/3.tri_clean/M9_raw_trimmed.fq.gz --outFileNamePrefix M9raw &> M9_raw.log

annonation: java -jar COMPSRA.jar -ref hg38 -ann -ac 1,2,3,4,5,6 -in ~/project2/7.clean_star/test/M9_raw_Aligned.out.bam -out ~/project2/7.clean_star/test/M9_raw_Aligned

Best wishes, Liang Wei

cougarlj commented 2 years ago

Dear liangwx332,

That should be fine. Otherwise, you can put STAR in the COMPSRA directory and change the name into version 2.5. So what's your question?

Best Wishes, Jiang Li

On Wed, Apr 6, 2022 at 7:56 PM liangwx332 @.***> wrote:

Hi，

I have an another question. Because speed of downloading star and hg38 genome is slow. So I could use my star to construct index, then use my star to align to genome but alignment parameters provided by your, finally use your scripts to annotation the alignment results. Code as following

Buildind indexes : STAR --genomeDir . --genomeFastaFiles hg38.fa --runMode genomeGenerate --runThreadN 3

Alingment: STAR --runThreadN 4 --runMode alignReads --outSAMtype BAM Unsorted --outSAMattributes Standard --readFilesCommand zcat --outSAMunmapped Within --outReadsUnmapped None --alignEndsType Local --outFilterMismatchNmax 1 --alignIntronMax 1 --alignIntronMin 2 --outFilterMultimapScoreRange 1 --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterMultimapNmax 1000000 --genomeDir /home/liangwei/project/1.pimran/index/test --readFilesIn /home/liangwei/project2/3.tri_clean/M9_raw_trimmed.fq.gz --outFileNamePrefix M9raw &> M9_raw.log

annonation: java -jar COMPSRA.jar -ref hg38 -ann -ac 1,2,3,4,5,6 -in ~/project2/7.clean_star/test/M9_raw_Aligned.out.bam -out ~/project2/7.clean_star/test/M9_raw_Aligned

Best wishes, Liang Wei

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liangwx332 commented 2 years ago

Dear Jiang Li, I'm really sorry for replying so late

Thank you very much for your reply. My question is whether I can align with the star I downloaded instead of the star provided by the software, and you have told me.

Best wishes, Liang Wei