Open hanjunjeon opened 6 years ago
Hi,
I am having problem sorting files. I tried to sort bed file and bam file using sort -k1,1 -k2,2n. However, I keep on getting the error message. Could you please help me on this matter?
cut -f 1 | uniq for bed file chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr1 chr20 chr21 chr22 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrM chrX
samtools view -H @HD VN:1.4 SO:coordinate @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr11_gl000202_random LN:40103 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 @SQ SN:chr16 LN:90354753 @SQ SN:chr17_ctg5_hap1 LN:1680828 @SQ SN:chr17 LN:81195210 @SQ SN:chr17_gl000203_random LN:37498 @SQ SN:chr17_gl000204_random LN:81310 @SQ SN:chr17_gl000205_random LN:174588 @SQ SN:chr17_gl000206_random LN:41001 @SQ SN:chr18 LN:78077248 @SQ SN:chr18_gl000207_random LN:4262 @SQ SN:chr19 LN:59128983 @SQ SN:chr19_gl000208_random LN:92689 @SQ SN:chr19_gl000209_random LN:159169 @SQ SN:chr1 LN:249250621 @SQ SN:chr1_gl000191_random LN:106433 @SQ SN:chr1_gl000192_random LN:547496 @SQ SN:chr20 LN:63025520 @SQ SN:chr21 LN:48129895 @SQ SN:chr21_gl000210_random LN:27682 @SQ SN:chr22 LN:51304566 @SQ SN:chr2 LN:243199373 @SQ SN:chr3 LN:198022430 @SQ SN:chr4_ctg9_hap1 LN:590426 @SQ SN:chr4 LN:191154276 @SQ SN:chr4_gl000193_random LN:189789 @SQ SN:chr4_gl000194_random LN:191469 @SQ SN:chr5 LN:180915260 @SQ SN:chr6_apd_hap1 LN:4622290 @SQ SN:chr6_cox_hap2 LN:4795371 @SQ SN:chr6_dbb_hap3 LN:4610396 @SQ SN:chr6 LN:171115067 @SQ SN:chr6_mann_hap4 LN:4683263 @SQ SN:chr6_mcf_hap5 LN:4833398 @SQ SN:chr6_qbl_hap6 LN:4611984 @SQ SN:chr6_ssto_hap7 LN:4928567 @SQ SN:chr7 LN:159138663 @SQ SN:chr7_gl000195_random LN:182896 @SQ SN:chr8 LN:146364022 @SQ SN:chr8_gl000196_random LN:38914 @SQ SN:chr8_gl000197_random LN:37175 @SQ SN:chr9 LN:141213431 @SQ SN:chr9_gl000198_random LN:90085 @SQ SN:chr9_gl000199_random LN:169874 @SQ SN:chr9_gl000200_random LN:187035 @SQ SN:chr9_gl000201_random LN:36148 @SQ SN:chrM LN:16571 @SQ SN:chrUn_gl000211 LN:166566 @SQ SN:chrUn_gl000212 LN:186858 @SQ SN:chrUn_gl000213 LN:164239 @SQ SN:chrUn_gl000214 LN:137718 @SQ SN:chrUn_gl000215 LN:172545 @SQ SN:chrUn_gl000216 LN:172294 @SQ SN:chrUn_gl000217 LN:172149 @SQ SN:chrUn_gl000218 LN:161147 @SQ SN:chrUn_gl000219 LN:179198 @SQ SN:chrUn_gl000220 LN:161802 @SQ SN:chrUn_gl000221 LN:155397 @SQ SN:chrUn_gl000222 LN:186861 @SQ SN:chrUn_gl000223 LN:180455 @SQ SN:chrUn_gl000224 LN:179693 @SQ SN:chrUn_gl000225 LN:211173 @SQ SN:chrUn_gl000226 LN:15008 @SQ SN:chrUn_gl000227 LN:128374 @SQ SN:chrUn_gl000228 LN:129120 @SQ SN:chrUn_gl000229 LN:19913 @SQ SN:chrUn_gl000230 LN:43691 @SQ SN:chrUn_gl000231 LN:27386 @SQ SN:chrUn_gl000232 LN:40652 @SQ SN:chrUn_gl000233 LN:45941 @SQ SN:chrUn_gl000234 LN:40531 @SQ SN:chrUn_gl000235 LN:34474 @SQ SN:chrUn_gl000236 LN:41934 @SQ SN:chrUn_gl000237 LN:45867 @SQ SN:chrUn_gl000238 LN:39939 @SQ SN:chrUn_gl000239 LN:33824 @SQ SN:chrUn_gl000240 LN:41933 @SQ SN:chrUn_gl000241 LN:42152 @SQ SN:chrUn_gl000242 LN:43523 @SQ SN:chrUn_gl000243 LN:43341 @SQ SN:chrUn_gl000244 LN:39929 @SQ SN:chrUn_gl000245 LN:36651 @SQ SN:chrUn_gl000246 LN:38154 @SQ SN:chrUn_gl000247 LN:36422 @SQ SN:chrUn_gl000248 LN:39786 @SQ SN:chrUn_gl000249 LN:38502 @SQ SN:chrX LN:155270560 @SQ SN:chrY LN:59373566 @PG ID:STAR PN:STAR VN:STAR_2.4.2a CL:STAR --runThreadN 8 --genomeDir /media/leelab/DATA/Downloads/Programs/SANJUAN/mapping_indexes/hg19_1/ --readFilesIn /media/leelab/DATA/RNA-seq/fastq/E13_D8_1_HJ7M2BBXX_S40_L006_R1_001.fastq.gz /media/leelab/DATA/RNA-seq/fastq/E13_D8_1_HJ7M2BBXX_S40_L006_R2_001.fastq.gz --readFilesCommand zcat --limitGenomeGenerateRAM 30064771072 --limitBAMsortRAM 30064771072 --outFileNamePrefix /media/leelab/DATA/SANJUAN/D8_RNPC3/MAPPING/D8_WT1 --outQSconversionAdd 0 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --outFilterMismatchNoverLmax 0.1 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --clip3pAdapterSeq AGATCGGAAGAGC --seedSearchStartLmax 50 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --twopassMode None @PG ID:STAR-5285621 PN:STAR VN:STAR_2.4.2a CL:STAR --runThreadN 8 --genomeDir /media/leelab/DATA/Downloads/Programs/SANJUAN/mapping_indexes/hg19_1/ --readFilesIn /media/leelab/DATA/RNA-seq/fastq/E13_D8_2_HJ7M2BBXX_S28_L004_R1_001.fastq.gz /media/leelab/DATA/RNA-seq/fastq/E13_D8_2_HJ7M2BBXX_S28_L004_R2_001.fastq.gz --readFilesCommand zcat --limitGenomeGenerateRAM 30064771072 --limitBAMsortRAM 30064771072 --outFileNamePrefix /media/leelab/DATA/SANJUAN/D8_RNPC3/MAPPING/D8_WT2 --outQSconversionAdd 0 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --outFilterMismatchNoverLmax 0.1 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --clip3pAdapterSeq AGATCGGAAGAGC --seedSearchStartLmax 50 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --twopassMode None @PG ID:STAR-61C1BBF7 PN:STAR VN:STAR_2.4.2a CL:STAR --runThreadN 8 --genomeDir /media/leelab/DATA/Downloads/Programs/SANJUAN/mapping_indexes/hg19_1/ --readFilesIn /media/leelab/DATA/RNA-seq/fastq/E13_D8_3_HJ7M2BBXX_S41_L006_R1_001.fastq.gz /media/leelab/DATA/RNA-seq/fastq/E13_D8_3_HJ7M2BBXX_S41_L006_R2_001.fastq.gz --readFilesCommand zcat --limitGenomeGenerateRAM 30064771072 --limitBAMsortRAM 30064771072 --outFileNamePrefix /media/leelab/DATA/SANJUAN/D8_RNPC3/MAPPING/D8_WT3 --outQSconversionAdd 0 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --outFilterMismatchNoverLmax 0.1 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --clip3pAdapterSeq AGATCGGAAGAGC --seedSearchStartLmax 50 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --twopassMode None @CO user command line: STAR --limitGenomeGenerateRAM 30064771072 --limitBAMsortRAM 30064771072 --outQSconversionAdd 0 --runThreadN 8 --genomeDir /media/leelab/DATA/Downloads/Programs/SANJUAN/mapping_indexes/hg19_1/ --readFilesIn /media/leelab/DATA/RNA-seq/fastq/E13_D8_1_HJ7M2BBXX_S40_L006_R1_001.fastq.gz /media/leelab/DATA/RNA-seq/fastq/E13_D8_1_HJ7M2BBXX_S40_L006_R2_001.fastq.gz --readFilesCommand zcat --clip3pAdapterSeq AGATCGGAAGAGC --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 50 --twopassMode None --outFileNamePrefix /media/leelab/DATA/SANJUAN/D8_RNPC3/MAPPING/D8_WT1 @CO user command line: STAR --limitGenomeGenerateRAM 30064771072 --limitBAMsortRAM 30064771072 --outQSconversionAdd 0 --runThreadN 8 --genomeDir /media/leelab/DATA/Downloads/Programs/SANJUAN/mapping_indexes/hg19_1/ --readFilesIn /media/leelab/DATA/RNA-seq/fastq/E13_D8_2_HJ7M2BBXX_S28_L004_R1_001.fastq.gz /media/leelab/DATA/RNA-seq/fastq/E13_D8_2_HJ7M2BBXX_S28_L004_R2_001.fastq.gz --readFilesCommand zcat --clip3pAdapterSeq AGATCGGAAGAGC --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 50 --twopassMode None --outFileNamePrefix /media/leelab/DATA/SANJUAN/D8_RNPC3/MAPPING/D8_WT2 @CO user command line: STAR --limitGenomeGenerateRAM 30064771072 --limitBAMsortRAM 30064771072 --outQSconversionAdd 0 --runThreadN 8 --genomeDir /media/leelab/DATA/Downloads/Programs/SANJUAN/mapping_indexes/hg19_1/ --readFilesIn /media/leelab/DATA/RNA-seq/fastq/E13_D8_3_HJ7M2BBXX_S41_L006_R1_001.fastq.gz /media/leelab/DATA/RNA-seq/fastq/E13_D8_3_HJ7M2BBXX_S41_L006_R2_001.fastq.gz --readFilesCommand zcat --clip3pAdapterSeq AGATCGGAAGAGC --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 50 --twopassMode None --outFileNamePrefix /media/leelab/DATA/SANJUAN/D8_RNPC3/MAPPING/D8_WT3
Thanks, Han Jun Jeon.
Hi,
I am having problem sorting files. I tried to sort bed file and bam file using sort -k1,1 -k2,2n. However, I keep on getting the error message. Could you please help me on this matter?
cut -f 1 | uniq for bed file chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr1 chr20 chr21 chr22 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrM chrX
samtools view -H
@HD VN:1.4 SO:coordinate
@SQ SN:chr10 LN:135534747
@SQ SN:chr11 LN:135006516
@SQ SN:chr11_gl000202_random LN:40103
@SQ SN:chr12 LN:133851895
@SQ SN:chr13 LN:115169878
@SQ SN:chr14 LN:107349540
@SQ SN:chr15 LN:102531392
@SQ SN:chr16 LN:90354753
@SQ SN:chr17_ctg5_hap1 LN:1680828
@SQ SN:chr17 LN:81195210
@SQ SN:chr17_gl000203_random LN:37498
@SQ SN:chr17_gl000204_random LN:81310
@SQ SN:chr17_gl000205_random LN:174588
@SQ SN:chr17_gl000206_random LN:41001
@SQ SN:chr18 LN:78077248
@SQ SN:chr18_gl000207_random LN:4262
@SQ SN:chr19 LN:59128983
@SQ SN:chr19_gl000208_random LN:92689
@SQ SN:chr19_gl000209_random LN:159169
@SQ SN:chr1 LN:249250621
@SQ SN:chr1_gl000191_random LN:106433
@SQ SN:chr1_gl000192_random LN:547496
@SQ SN:chr20 LN:63025520
@SQ SN:chr21 LN:48129895
@SQ SN:chr21_gl000210_random LN:27682
@SQ SN:chr22 LN:51304566
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4_ctg9_hap1 LN:590426
@SQ SN:chr4 LN:191154276
@SQ SN:chr4_gl000193_random LN:189789
@SQ SN:chr4_gl000194_random LN:191469
@SQ SN:chr5 LN:180915260
@SQ SN:chr6_apd_hap1 LN:4622290
@SQ SN:chr6_cox_hap2 LN:4795371
@SQ SN:chr6_dbb_hap3 LN:4610396
@SQ SN:chr6 LN:171115067
@SQ SN:chr6_mann_hap4 LN:4683263
@SQ SN:chr6_mcf_hap5 LN:4833398
@SQ SN:chr6_qbl_hap6 LN:4611984
@SQ SN:chr6_ssto_hap7 LN:4928567
@SQ SN:chr7 LN:159138663
@SQ SN:chr7_gl000195_random LN:182896
@SQ SN:chr8 LN:146364022
@SQ SN:chr8_gl000196_random LN:38914
@SQ SN:chr8_gl000197_random LN:37175
@SQ SN:chr9 LN:141213431
@SQ SN:chr9_gl000198_random LN:90085
@SQ SN:chr9_gl000199_random LN:169874
@SQ SN:chr9_gl000200_random LN:187035
@SQ SN:chr9_gl000201_random LN:36148
@SQ SN:chrM LN:16571
@SQ SN:chrUn_gl000211 LN:166566
@SQ SN:chrUn_gl000212 LN:186858
@SQ SN:chrUn_gl000213 LN:164239
@SQ SN:chrUn_gl000214 LN:137718
@SQ SN:chrUn_gl000215 LN:172545
@SQ SN:chrUn_gl000216 LN:172294
@SQ SN:chrUn_gl000217 LN:172149
@SQ SN:chrUn_gl000218 LN:161147
@SQ SN:chrUn_gl000219 LN:179198
@SQ SN:chrUn_gl000220 LN:161802
@SQ SN:chrUn_gl000221 LN:155397
@SQ SN:chrUn_gl000222 LN:186861
@SQ SN:chrUn_gl000223 LN:180455
@SQ SN:chrUn_gl000224 LN:179693
@SQ SN:chrUn_gl000225 LN:211173
@SQ SN:chrUn_gl000226 LN:15008
@SQ SN:chrUn_gl000227 LN:128374
@SQ SN:chrUn_gl000228 LN:129120
@SQ SN:chrUn_gl000229 LN:19913
@SQ SN:chrUn_gl000230 LN:43691
@SQ SN:chrUn_gl000231 LN:27386
@SQ SN:chrUn_gl000232 LN:40652
@SQ SN:chrUn_gl000233 LN:45941
@SQ SN:chrUn_gl000234 LN:40531
@SQ SN:chrUn_gl000235 LN:34474
@SQ SN:chrUn_gl000236 LN:41934
@SQ SN:chrUn_gl000237 LN:45867
@SQ SN:chrUn_gl000238 LN:39939
@SQ SN:chrUn_gl000239 LN:33824
@SQ SN:chrUn_gl000240 LN:41933
@SQ SN:chrUn_gl000241 LN:42152
@SQ SN:chrUn_gl000242 LN:43523
@SQ SN:chrUn_gl000243 LN:43341
@SQ SN:chrUn_gl000244 LN:39929
@SQ SN:chrUn_gl000245 LN:36651
@SQ SN:chrUn_gl000246 LN:38154
@SQ SN:chrUn_gl000247 LN:36422
@SQ SN:chrUn_gl000248 LN:39786
@SQ SN:chrUn_gl000249 LN:38502
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@PG ID:STAR PN:STAR VN:STAR_2.4.2a CL:STAR --runThreadN 8 --genomeDir /media/leelab/DATA/Downloads/Programs/SANJUAN/mapping_indexes/hg19_1/ --readFilesIn /media/leelab/DATA/RNA-seq/fastq/E13_D8_1_HJ7M2BBXX_S40_L006_R1_001.fastq.gz /media/leelab/DATA/RNA-seq/fastq/E13_D8_1_HJ7M2BBXX_S40_L006_R2_001.fastq.gz --readFilesCommand zcat --limitGenomeGenerateRAM 30064771072 --limitBAMsortRAM 30064771072 --outFileNamePrefix /media/leelab/DATA/SANJUAN/D8_RNPC3/MAPPING/D8_WT1 --outQSconversionAdd 0 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --outFilterMismatchNoverLmax 0.1 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --clip3pAdapterSeq AGATCGGAAGAGC --seedSearchStartLmax 50 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --twopassMode None
@PG ID:STAR-5285621 PN:STAR VN:STAR_2.4.2a CL:STAR --runThreadN 8 --genomeDir /media/leelab/DATA/Downloads/Programs/SANJUAN/mapping_indexes/hg19_1/ --readFilesIn /media/leelab/DATA/RNA-seq/fastq/E13_D8_2_HJ7M2BBXX_S28_L004_R1_001.fastq.gz /media/leelab/DATA/RNA-seq/fastq/E13_D8_2_HJ7M2BBXX_S28_L004_R2_001.fastq.gz --readFilesCommand zcat --limitGenomeGenerateRAM 30064771072 --limitBAMsortRAM 30064771072 --outFileNamePrefix /media/leelab/DATA/SANJUAN/D8_RNPC3/MAPPING/D8_WT2 --outQSconversionAdd 0 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --outFilterMismatchNoverLmax 0.1 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --clip3pAdapterSeq AGATCGGAAGAGC --seedSearchStartLmax 50 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --twopassMode None
@PG ID:STAR-61C1BBF7 PN:STAR VN:STAR_2.4.2a CL:STAR --runThreadN 8 --genomeDir /media/leelab/DATA/Downloads/Programs/SANJUAN/mapping_indexes/hg19_1/ --readFilesIn /media/leelab/DATA/RNA-seq/fastq/E13_D8_3_HJ7M2BBXX_S41_L006_R1_001.fastq.gz /media/leelab/DATA/RNA-seq/fastq/E13_D8_3_HJ7M2BBXX_S41_L006_R2_001.fastq.gz --readFilesCommand zcat --limitGenomeGenerateRAM 30064771072 --limitBAMsortRAM 30064771072 --outFileNamePrefix /media/leelab/DATA/SANJUAN/D8_RNPC3/MAPPING/D8_WT3 --outQSconversionAdd 0 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --outFilterMismatchNoverLmax 0.1 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --clip3pAdapterSeq AGATCGGAAGAGC --seedSearchStartLmax 50 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --twopassMode None
@CO user command line: STAR --limitGenomeGenerateRAM 30064771072 --limitBAMsortRAM 30064771072 --outQSconversionAdd 0 --runThreadN 8 --genomeDir /media/leelab/DATA/Downloads/Programs/SANJUAN/mapping_indexes/hg19_1/ --readFilesIn /media/leelab/DATA/RNA-seq/fastq/E13_D8_1_HJ7M2BBXX_S40_L006_R1_001.fastq.gz /media/leelab/DATA/RNA-seq/fastq/E13_D8_1_HJ7M2BBXX_S40_L006_R2_001.fastq.gz --readFilesCommand zcat --clip3pAdapterSeq AGATCGGAAGAGC --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 50 --twopassMode None --outFileNamePrefix /media/leelab/DATA/SANJUAN/D8_RNPC3/MAPPING/D8_WT1
@CO user command line: STAR --limitGenomeGenerateRAM 30064771072 --limitBAMsortRAM 30064771072 --outQSconversionAdd 0 --runThreadN 8 --genomeDir /media/leelab/DATA/Downloads/Programs/SANJUAN/mapping_indexes/hg19_1/ --readFilesIn /media/leelab/DATA/RNA-seq/fastq/E13_D8_2_HJ7M2BBXX_S28_L004_R1_001.fastq.gz /media/leelab/DATA/RNA-seq/fastq/E13_D8_2_HJ7M2BBXX_S28_L004_R2_001.fastq.gz --readFilesCommand zcat --clip3pAdapterSeq AGATCGGAAGAGC --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 50 --twopassMode None --outFileNamePrefix /media/leelab/DATA/SANJUAN/D8_RNPC3/MAPPING/D8_WT2
@CO user command line: STAR --limitGenomeGenerateRAM 30064771072 --limitBAMsortRAM 30064771072 --outQSconversionAdd 0 --runThreadN 8 --genomeDir /media/leelab/DATA/Downloads/Programs/SANJUAN/mapping_indexes/hg19_1/ --readFilesIn /media/leelab/DATA/RNA-seq/fastq/E13_D8_3_HJ7M2BBXX_S41_L006_R1_001.fastq.gz /media/leelab/DATA/RNA-seq/fastq/E13_D8_3_HJ7M2BBXX_S41_L006_R2_001.fastq.gz --readFilesCommand zcat --clip3pAdapterSeq AGATCGGAAGAGC --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 50 --twopassMode None --outFileNamePrefix /media/leelab/DATA/SANJUAN/D8_RNPC3/MAPPING/D8_WT3
Thanks, Han Jun Jeon.