Entering edit mode
5.2 years ago
sneha.preha7
•
0
My reads names are not identical even after treating with "awk cmd "
here are the commands that I used
awk '{{print (NR%4 == 1) ? "@1_" ++i "/1": $0}}' Read_1.fastq > Raed_1_renamed.fastq
awk '{{print (NR%4 == 1) ? "@2_" ++i "/2": $0}}' Raed_2.fastq > Raed_2_renamed.fastq
after this I have perform the Triimomatic cmd for trimming but in the out put I got very less number of reverse read here is a cmd
java -jar /share/apps/Trimmomatic-0.38/trimmomatic-0.38.jar PE -phred33 Read_1_renamed.fastq Read_2_renamed.fastq FP_Read_1.fastq FU_Read_1.fastq RP_Read_2.fastq RU_Raed_2.fastq ILLUMINACLIP:/share/apps/Trimmomatic-0.38/adapters/TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:10 MINLEN:36
Output:-
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
Using Long Clipping Sequence: 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using Long Clipping Sequence: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Read Pairs: ****47190247 Both Surviving: 44940671 (95.23%) Forward Only Surviving: 1504722 (3.19%) Reverse Only Surviving: 365037 (0.77%) Dropped: 379817 (0.80%)****
TrimmomaticPE: Completed successfully
after this the size of the file is
Read_1_renamed.fastq 9.7 GB Read_2_renamed.fastq 9.7 GB
FP_Read_1.fastq 8.3G FU_Read_1.fastq 253M RP_Read_2.fastq 8.3G RU_Raed_2.fastq 62M
After this I tried to run the trinity and it was aborted stating the following error
/share/apps/trinityrnaseq-Trinity-v2.8.3/Trinity --seqType fq --left FP_Read_1.fastq,FU_Read_1.fastq --right RP_Read_2.fastq,RU_Raed_2.fastq --CPU 10 --max_memory 96G
Error, pairs.K25.stats is empty. Be sure to check your fastq reads and ensure that the read names are identical except for the /1 or /2 designation. at /share/apps/trinityrnaseq-Trinity-v2.8.3/util/insilico_read_normalization.pl line 921.
later i have checked tried to see the head so I found this
[sneharl@compute-0-8 nep11]$ head RP_Read_2.fastq
@2_13/2
ACATAATCTCACTCGACGTACCAGGCATGAGGAGGGAGGATGTCAAGATAGAGGTGGAGGAGAACAGGGTGCTGAGGGTGAGCGGAGAGAG
+
FHHJJIIJJGIJJIJ?HIFFHJCHIIGDHBEH<DGA@FHCGC=AAEHEFDFFFE6=AABBB@?ADA?AB5?@CCCDDD088AA<<<958<<
@2_15/2
TCAATTCATCAACAACCTTAGATCTCAACTCATCAGCAAGCTCTTTCTGGGCAGTATCACTTGGAGATTTCTTCCCTGTCCTAAGACAAGC
+
HHHJJJJJIJJIJJIJJJJJJIIIIIJJJIGJIJJJJIJHHIIJIJJHIJJJFIDHIJJJJIJIJJHHHHHHFFFFFF;AECCEDDDDDDD
@2_16/2
GCAGAAACAGAAGGGTAATTCAGTGCTACTGCATCAAAGACTGTCTGCCTGACACAGTTGGGAGTTTGAACACCAACAATAACCAAGCTAT
[sneharl@compute-0-8 nep11]$ head RU_Raed_2.fastq
@2_78/2
AAGCATCACGTCAAATGAACAGCCGTACAATACGCAGCGCACCTTATTCCAACGCCTTTTCTCGTCAACGATTTACGATTGCAAATTATCA
+
HHHJJJIJJJJJJJJJJIJJJJJJJIJIJIIJEHJJIJJIHIHHHHHHFFFFFDDDDDDDDDDDDDDDDDDDDDDEBDDD?CCDDDDDEDC
@2_682/2
AATACAAGAAAATTTCGTCTCATTCAAAAGTCCCTT
+
A?D<<<:AFF3<FEFI@+A8?4?E@ECFC3*1?**0
@2_735/2
ACTATGACAGATATCGATACCGATATTTTCATCCATCCACCGGACCCAAAATATACTACCAAAAAGGAAATGATTTCTCTTCACTTCGTTC
I have tried to check the file left.fa.K25.stats and right.fa.K25.stats
[sneharl@compute-0-8 tmp_normalized_reads]$ head left.fa.K25.stats
273661 257154 60829.4 23.6548 1_5/1 thread:0
3393 3310.83 452.798 13.6763 1_6/1 thread:4
551157 378893 292184 77.1153 1_4/1 thread:2
247465 248536 12803.3 5.15147 1_1/1 thread:1
2550 2421.5 783.635 32.3616 1_3/1 thread:3
715265 769537 114199 14.8399 1_9/1 thread:2
50212 49096.3 8357.57 17.0228 1_8/1 thread:4
888228 835519 213339 25.5337 1_10/1 thread:1
913960 907977 68618 7.55724 1_11/1 thread:3
913960 908888 69092.1 7.60182 1_7/1 thread:0
[sneharl@compute-0-8 tmp_normalized_reads]$ head right.fa.K25.stats
281168 278462 7324.79 2.63045 2_1/2 thread:3
2232 2306 146.529 6.35423 2_3/2 thread:0
3746 3771.5 88.5557 2.34802 2_6/2 thread:2
332464 329362 16988.3 5.15796 2_5/2 thread:4
325543 322963 16191 5.01327 2_4/2 thread:1
920338 922948 10396.2 1.12641 2_7/2 thread:3
62646 62614.5 994.886 1.58891 2_8/2 thread:0
1138774 1.14581e+06 38648.5 3.37302 2_9/2 thread:2
800599 811590 45665.9 5.62673 2_10/2 thread:4
821097 820930 31654.2 3.8559 2_11/2 thread:1
[sneharl@compute-0-8 tmp_normalized_reads]$
Please help me in this regard
