Question: error in trinity
0
gravatar for fatimarasool135
9 months ago by
fatimarasool13560 wrote:

hi , I am doing denovo assembly by using trinity. data is not from SRA . .but got these error .how can i resolve it ?

> 
> Error, not recognizing read name formatting: [NS500786:42:HA1AGGAAGACCACGAATTGCCTTGTGAAEEAEEEGXX:2:1210G:7930EAE/EEEEEAE/EAEEEEEE/AA<A/E/AE/EE/EEECGCAGATG13379EAAEEEEAAGAAAAA]

>If your data come from SRA, be sure to dump the fastq file like so:

  SRA_TOOLKIT/fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files file.sra
rna-seq alignment assembly • 228 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by fatimarasool13560

fatimarasool135 please share the complete command that you executed

ADD REPLYlink written 9 months ago by lakhujanivijay5.1k

Hi, I have run this command

Trinity --seqType fq --left /home/bioinfo/fatima/G2_forward_paired.fq --right /home/bioinfo/fatima/G2_reverse_paired.fq --max_memory 102G --output G2_trinity

ADD REPLYlink written 9 months ago by fatimarasool13560

the fastq file look like that

head G2_forward_paired.fq

@NS500786:42:HW75GBGXX:1:21307:2729:10394 1:N:0:TCCGGAGA+AGGATAGG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEE66E6666
@NS500786:42:HW75GBGXX:4:11411:6035:6026 1:N:0:GCCGGAGA+AGGATAGG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
AEE6EAEEEEEEEEEEEEEEA6E6E6EEEA6666666666666666666/6
@NS500786:42:HW75GBGXX:3:12405:6583:13106 1:N:0:TCCGGAGA+AGGATAGG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

G2_reverse_paired.fq

@NS500786:42:HW75GBGXX:1:21307:2729:10394 2:N:0:TCCGGAGA+AGGATAGG
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+
AAAAAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEA
@NS500786:42:HW75GBGXX:4:11411:6035:6026 2:N:0:GCCGGAGA+AGGATAGG
ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+
6AAAA//AAA/AA///<A<A/A<AA<EEA//A</<<66/<//A6/<</6A66<<66/</66//6
@NS500786:42:HW75GBGXX:3:12405:6583:13106 2:N:0:TCCGGAGA+AGGATAGG
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
ADD REPLYlink modified 9 months ago by lakhujanivijay5.1k • written 9 months ago by fatimarasool13560

Could you at least spell the name of the tool you are using correctly? Please put some more effort into your questions.

ADD REPLYlink written 9 months ago by WouterDeCoster44k
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